diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 163e73c918005daa41d1ba0ba3fe54200b43dd89..65663b8d7d0186e3bdfcada34ebdbcc449b26367 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -54,4 +54,4 @@ python3.10:
stage: Static Analysis and Test
script:
- python -m unittest
- coverage: '/TOTAL.+ ([0-9]{1,3}%)/'
+ coverage: '/TOTAL.+ ([0-9]{1,3}%)/'
\ No newline at end of file
diff --git a/README.rst b/README.rst
index 23aeee58c0cd2d5d92273a5f4e3e2b92d10754c8..055130e1cefc49a0dac0b32f6309aa975a896eaf 100644
--- a/README.rst
+++ b/README.rst
@@ -9,12 +9,13 @@ lemi2seed
- ``lemi2seed -h``
- ``lemi2seed -d path2data -qc`` *(run lemi2seed in "quality control" mode)*
- ``lemi2seed -d path2data -g`` *(run lemi2seed in "gui only" mode)*
+ - ``lemi2seed -d path2data -g -s path2savedmd`` *(run lemi2seed in "gui only" mode after loading previously saved metadata fields)*
- ``lemi2seed -d path2data -m path2metadata`` *(run lemi2seed in "field sheet and gui" mode)*
The "quality control" mode allows to quickly convert LEMI data to day-long mseed files. The GUI and handling of metadata are bypassed.
- In the "gui only" mode, metadata are entered only using the GUI.
+ In the "gui only" mode, metadata are entered/modified using the GUI only.
- In the "field sheet and gui" mode, metadata are prepopulated from parsing the provided field sheets.
+ In the "field sheet and gui" mode, metadata are prepopulated from parsing the user-provided field sheets and modified using the GUI.
- **License**: GNU General Public License v3 (GPLv3)
diff --git a/conda.recipe/meta.yaml b/conda.recipe/meta.yaml
index da55d97f9aeeeb30cffb4e26904c4553a75a914b..b7a9211f68e78d7005b8ba2d3b7d5ae6a29b048f 100644
--- a/conda.recipe/meta.yaml
+++ b/conda.recipe/meta.yaml
@@ -1,6 +1,6 @@
package:
name: lemi2seed
- version: 2022.319
+ version: 2023.1.3.1
source:
path: ../
diff --git a/lemi2seed/__init__.py b/lemi2seed/__init__.py
index ace4ceb11ea9b66810f00d2b4785b782692471bb..8b701fe61092b9575cf7aaf196a473bdb35980c3 100644
--- a/lemi2seed/__init__.py
+++ b/lemi2seed/__init__.py
@@ -2,6 +2,6 @@
"""Top-level package for lemi2seed."""
-__author__ = """IRIS PASSCAL"""
+__author__ = """EPIC"""
__email__ = 'software-support@passcal.nmt.edu'
-__version__ = '2022.319'
+__version__ = '2023.1.3.1'
diff --git a/lemi2seed/config/config.ini b/lemi2seed/config/config.ini
index 1ff472e6fa2ce9d0210cccacb3dff677016ecda0..9b5c45837ea06ea25c6e59741816e71737f91b3e 100644
--- a/lemi2seed/config/config.ini
+++ b/lemi2seed/config/config.ini
@@ -1,7 +1,7 @@
[software]
author = Maeva Pourpoint
name = lemi2seed
-version = 2022.319
+version = 2023.1.3.1
[sheets]
header = A1
@@ -17,16 +17,13 @@ credential_sheet = Credential Sheet for Long-Period Magnetotelluric Instrument
[[credential_sheet]]
acq_by_author = B4
acq_by_comments = B5
- citation_dataset_doi = B6
- country = B7
- geo_name = B8
- name = B9
- project = B10
- project_lead_author = B11
- project_lead_email = B12
- project_lead_organization = B13
- restricted_status = B15
- summary = B14
+ country = B6
+ geo_name = B7
+ name = B8
+ project = B9
+ project_lead_author = B10
+ project_lead_organization = B11
+ summary = B12
[Sta]
[[install_sheet]]
@@ -35,31 +32,27 @@ credential_sheet = Credential Sheet for Long-Period Magnetotelluric Instrument
declination_model = H10
declination_val = H9
elev = G98
+ end = B101
lat = C98
lon = E98
orientation_method = D11
orientation_reference_frame = B11
start = B100
[[credential_sheet]]
- geo_name = B18
- restricted_status = B22
- submitter_author = B19
- submitter_email = B20
- submitter_organization = B21
- [[removal_sheet]]
- comments =
- end =
+ geo_name = B15
+ submitter_author = B16
+ submitter_organization = B17
[Run]
[[install_sheet]]
comps_rec = B12
datalogger_sn = B16
[[credential_sheet]]
- acq_by_author = B25
- acq_by_comments = B26
- comments = B29
- md_by_author = B27
- md_by_comments = B28
+ acq_by_author = B20
+ acq_by_comments = B21
+ comments = B24
+ md_by_author = B22
+ md_by_comments = B23
[Elec]
[[install_sheet]]
@@ -75,9 +68,6 @@ credential_sheet = Credential Sheet for Long-Period Magnetotelluric Instrument
inst_specs = B26
meas_azimuth = F40, F41, F42, F43
meas_tilt = H40, H41, H42, H43
- [[removal_sheet]]
- contact_resistance_end =
- dc_end =
[Mag]
[[install_sheet]]
diff --git a/lemi2seed/data_conversion.py b/lemi2seed/data_conversion.py
index 260ddfdf62f691a1a04140efbaa4389756c7345b..27a1fbe9ff50c8f58865d8706d4688793cf7562a 100644
--- a/lemi2seed/data_conversion.py
+++ b/lemi2seed/data_conversion.py
@@ -90,9 +90,12 @@ def write_daylong_mseed(lemi_data: LemiData) -> None:
filename = path2mseed.joinpath('.'.join([tr_day.stats.station, tr_day.stats.network,
loc, cha, str(year), str(day).zfill(3)]))
if filename.is_file():
- logger.info("The mseed file {} already exists. Merging to it.".format(filename))
+ logger.info("The mseed file {} already exists. Merging to "
+ "it. There will be no duplication of existing data."
+ .format(filename))
st_day = handle_existing_mseed_file(st_day, filename)
st_day.merge(-1)
+ logger.info("Writing day-long mseed file: {}.".format(filename))
st_day.write(filename, format='MSEED')
logger.info("Writing of day-long mseed files successfully completed!")
@@ -135,7 +138,7 @@ def write_log_file(lemi_data: LemiData) -> None:
def files.
"""
log_file = get_log_filename(lemi_data)
- logger.info("Writing calibration coefficients in log file {}.".format(log_file))
+ logger.info("Writing calibration coefficients in log file: {}.".format(log_file))
def_info = parse_def_files(lemi_data.def_files)
with open(log_file, 'w') as fout:
fout.write(f"{config['software']['name']}: v{config['software']['version']} - "
diff --git a/lemi2seed/gui_view.py b/lemi2seed/gui_view.py
index f26a5995e2add9f28db9038063a6dc39b911534e..2b382b3213a11b528ac9a82a5ffb1fc554e3e06c 100644
--- a/lemi2seed/gui_view.py
+++ b/lemi2seed/gui_view.py
@@ -19,6 +19,7 @@ from lemi2seed.gui_widgets import (load_ui, BaseWidget, NetWidgets,
get_channel_widgets)
from lemi2seed.lemi_metadata import LemiMetadata
from lemi2seed.logging import parse_config_ini, setup_logger
+from lemi2seed.metadata_category import MSG_MAP
from lemi2seed.metadata_conversion import write_stationxml
from lemi2seed.utils import get_e_ids, get_run_list, NUM_E_CHA_MAX
@@ -135,12 +136,15 @@ class LemiWindow(*load_ui('mainwindow.ui')):
for run_id in run_list:
self.update_elec_selection_forms(run_id)
- def load_md(self):
+ def load_md(self, path2savedmd=None):
"""Load previously saved metadata model."""
- filename, _ = QtWidgets.QFileDialog.getOpenFileName(parent=self,
- caption='Select metadata file to open',
- dir=str(Path.cwd()),
- filter='Metadata file (*.pkl)')
+ if path2savedmd:
+ filename = str(path2savedmd)
+ else:
+ filename, _ = QtWidgets.QFileDialog.getOpenFileName(parent=self,
+ caption='Select metadata file to open',
+ dir=str(Path.cwd()),
+ filter='Metadata file (*.pkl)')
if filename:
text = "Loading previously saved metadata..."
details = ("If you are creating mseed and StationXML files for a "
@@ -162,6 +166,12 @@ class LemiWindow(*load_ui('mainwindow.ui')):
if filename:
self.lemi_md.save_md(filename)
+ def get_run_widgets(self, run_id):
+ return getattr(self, f'run_{run_id}_widgets')
+
+ def set_run_widgets(self, run_id, val):
+ setattr(self, f'run_{run_id}_widgets', val)
+
def set_num_runs_form(self):
"""
Set up number of runs form. There is one form for all runs. This form
@@ -189,7 +199,7 @@ class LemiWindow(*load_ui('mainwindow.ui')):
starttimes = [x['starttime'] for x in self.lemi_data.data_np]
# Add 1 to ind_run since run_nums (number of given run) starts at 1
starttime = starttimes[run_nums.index(ind_run + 1)]
- starttime_reformat = starttime.datetime.strftime("%m/%d/%Y %H:%M:%S")
+ starttime_reformat = starttime.datetime.strftime("%Y-%m-%d %H:%M:%S")
# Set up layout form
layout_run_starttime = QtWidgets.QFormLayout()
uiRunStarttime = QtWidgets.QLineEdit()
@@ -201,11 +211,78 @@ class LemiWindow(*load_ui('mainwindow.ui')):
layout_run_starttime.setFormAlignment(QtCore.Qt.AlignLeft)
return layout_run_starttime
- def get_run_widgets(self, run_id):
- return getattr(self, f'run_{run_id}_widgets')
+ def submit_run_cha_md(self, run_id, elec_bool=False, mag_bool=False):
+ """
+ Submit run and channel metadata entries provided by the user up to this
+ point before checking validity of metadata fields to be copied.
+ Submit policy set in BaseWidget is Manual.
+ """
+ # -- Run --
+ run = self.get_run_widgets(run_id)
+ run.mapper.submit()
+ # -- Electric --
+ if elec_bool:
+ name = f'run_{run_id}_num_e_pairs'
+ num_e_pairs_submit = getattr(self, name, NUM_E_CHA_MAX)
+ for ind in range(1, num_e_pairs_submit + 1):
+ e_pair = self.get_elec_pair_widgets(run_id, ind)
+ e_pair.mapper.submit()
+ # -- Magnetic --
+ if mag_bool:
+ mag = self.get_mag_widgets(run_id)
+ mag.mapper.submit()
- def set_run_widgets(self, run_id, val):
- setattr(self, f'run_{run_id}_widgets', val)
+ def check_before_reset(self, run_id_same_as, run_id, type_):
+ """
+ Check/Validate metadata fields for both runs before copying electric or
+ magnetic metadata fields from one run to the other.
+ """
+ cha_type = MSG_MAP[type_.capitalize()]
+ logger.info(f"{'-'*20} Checking metadata fields for run '{run_id_same_as}' "
+ f"before copying {cha_type} metadata fields from run "
+ f"'{run_id_same_as}' to run '{run_id}'. Any incomplete or "
+ "invalid metadata fields may prevent the auto-filling "
+ "process from succesfully completing. Look for potential"
+ f"error messages below {'-'*20}.")
+ self.validate_run(run_id_same_as)
+ if cha_type != 'run':
+ validate_method = f"validate_{type_}"
+ methodcaller(validate_method, run_id_same_as)(self)
+ logger.info(f"{'-'*20} End of metadata field checks for run "
+ f"'{run_id_same_as}' {'-'*20}.")
+
+ def reset_run_model(self, run_id_same_as, run_id):
+ """
+ Reset current run metadata model based on a user-selected run id.
+ Called when selecting the "Same as run" option for run_id > a.
+ """
+ self.submit_run_cha_md(run_id_same_as)
+ self.check_before_reset(run_id_same_as, run_id, 'run')
+ md = self.lemi_md.for_gui
+ key = f'Run_{run_id}'
+ key_same_as = f'Run_{run_id_same_as}'
+ md['Run'][key].update(md['Run'][key_same_as])
+ model = TreeModel(("Field", "Value"), md)
+ run = self.get_run_widgets(run_id)
+ run.set_model(model, f'Run_{run_id}')
+
+ def set_cha_same_as_forms(self, cha_type, run_id):
+ """
+ Set up "same as run" form.
+ Called when there is more than one run and selecting the "Same as run option.
+ """
+ run_ids = self.run_list[:self.run_list.index(run_id)]
+ layout_same_as = QtWidgets.QFormLayout()
+ uiRunIdSameAs = QtWidgets.QComboBox()
+ uiRunIdSameAs.addItems(run_ids)
+ for ind, id in enumerate(run_ids):
+ tip_msg = (f'Same {cha_type} metadata field values as Run {id}.')
+ uiRunIdSameAs.setItemData(ind, tip_msg, QtCore.Qt.ToolTipRole)
+ reset_method = f'reset_{cha_type}_model'
+ uiRunIdSameAs.textActivated.connect(lambda text, val=run_id: methodcaller(reset_method, text, val)(self))
+ layout_same_as.addRow('Same as run', uiRunIdSameAs)
+ layout_same_as.setFormAlignment(QtCore.Qt.AlignLeft)
+ return layout_same_as
def set_run_editor_forms(self):
"""Set up run editor form. There is one form per run id."""
@@ -217,9 +294,14 @@ class LemiWindow(*load_ui('mainwindow.ui')):
self.sta_widgets.uiRunsEditor.addWidget(uiTabs)
for run_id in self.run_list:
uiRun = QtWidgets.QWidget()
- layout_run = QtWidgets.QVBoxLayout()
+ layout_run_option = QtWidgets.QHBoxLayout()
layout_run_starttime = self.set_run_starttime_form(run_id)
- layout_run.addLayout(layout_run_starttime)
+ layout_run_option.addLayout(layout_run_starttime)
+ if run_id != 'a':
+ layout_run_same_as = self.set_cha_same_as_forms('run', run_id)
+ layout_run_option.addLayout(layout_run_same_as)
+ layout_run = QtWidgets.QVBoxLayout()
+ layout_run.addLayout(layout_run_option)
layout_run.addSpacing(5)
self.set_run_widgets(run_id, RunWidgets(self))
layout_run.addWidget(self.get_run_widgets(run_id))
@@ -319,56 +401,18 @@ class LemiWindow(*load_ui('mainwindow.ui')):
electrode pairs can be infered from the 'components recorded' metadata
field.
"""
- e_comps = self.lemi_md.get_comps_rec('E', run_id, msg=False) if self.lemi_md.run else []
+ e_comps = self.lemi_md.get_comps_rec('E', run_id) if self.lemi_md.run else []
num_e_pairs = len(e_comps)
uiNumEPairs = getattr(self, f'run_{run_id}_num_e_pairs_widgets')
uiNumEPairs.setCurrentIndex(VALID_NUM_E_PAIRS.index(num_e_pairs))
self.update_elec_pair_forms(num_e_pairs, run_id)
- def submit_run_cha_md(self, run_list, elec_bool=False, mag_bool=False):
- """Submit run and channel metadata entries."""
- for run_id in run_list:
- # -- Run --
- run = self.get_run_widgets(run_id)
- run.mapper.submit()
- # -- Electric --
- if elec_bool:
- name = f'run_{run_id}_num_e_pairs'
- num_e_pairs_submit = getattr(self, name, NUM_E_CHA_MAX)
- for ind in range(1, num_e_pairs_submit + 1):
- e_pair = self.get_elec_pair_widgets(run_id, ind)
- e_pair.mapper.submit()
- # -- Magnetic --
- if mag_bool:
- mag = self.get_mag_widgets(run_id)
- mag.mapper.submit()
-
- def check_before_reset(self, run_id_same_as, run_id, type_):
- """
- Check/Validate metadata fields for both runs before copying electric or
- magnetic metadata fields from one run to the other.
- """
- cha_type = 'electric' if type_ == 'elec' else 'magnetic'
- logger.info(f"{'-'*20} Checking metadata fields for runs '{run_id_same_as}' "
- f"and '{run_id}' before copying {cha_type} metadata fields "
- f"from run '{run_id_same_as}' to run '{run_id}'. Any "
- "incomplete or invalid metadata fields may prevent the "
- "auto-filling process from succesfully completing. Look "
- f"for potential error messages below {'-'*20}.")
- self.validate_run(run_id_same_as)
- self.validate_run(run_id)
- validate_method = f"validate_{type_}"
- methodcaller(validate_method, run_id_same_as)(self)
- logger.info(f"{'-'*20} End of metadata field checks for runs "
- f"'{run_id_same_as}' and '{run_id}' {'-'*20}.")
-
def reset_elec_model(self, run_id_same_as, run_id):
"""
- Reset current electric metadata model for a given run id.
- Called when there is more than one run and selecting the "Same as run"
- option for run_id > a.
+ Reset current electric metadata model based on a user-selected run id.
+ Called when selecting the "Same as run" option for run_id > a.
"""
- self.submit_run_cha_md([run_id_same_as, run_id], elec_bool=True)
+ self.submit_run_cha_md(run_id_same_as, elec_bool=True)
self.check_before_reset(run_id_same_as, run_id, 'elec')
md = self.lemi_md.for_gui
for ind_cha in range(1, NUM_E_CHA_MAX + 1):
@@ -380,25 +424,6 @@ class LemiWindow(*load_ui('mainwindow.ui')):
e_pair = self.get_elec_pair_widgets(run_id, ind_cha)
e_pair.set_model(model, f'Run_{run_id}_Elec_Pair_{ind_cha}')
- def set_cha_same_as_forms(self, cha_type, run_id):
- """
- Set up "same as run" form.
- Called when there is more than one run and selecting the "Same as run"
- option for run id > a.
- """
- run_ids = self.run_list[:self.run_list.index(run_id)]
- layout_elec_same_as = QtWidgets.QFormLayout()
- uiRunIdSameAs = QtWidgets.QComboBox()
- uiRunIdSameAs.addItems(run_ids)
- for ind, id in enumerate(run_ids):
- tip_msg = (f'Same metadata field values as Run {id}.')
- uiRunIdSameAs.setItemData(ind, tip_msg, QtCore.Qt.ToolTipRole)
- reset_method = f'reset_{cha_type}_model'
- uiRunIdSameAs.textActivated.connect(lambda text, val=run_id: methodcaller(reset_method, text, val)(self))
- layout_elec_same_as.addRow('Same as run', uiRunIdSameAs)
- layout_elec_same_as.setFormAlignment(QtCore.Qt.AlignLeft)
- return layout_elec_same_as
-
def set_elec_editor_forms(self, ElecWidgets):
"""
Set up the electric editor form for all runs.
@@ -433,11 +458,10 @@ class LemiWindow(*load_ui('mainwindow.ui')):
def reset_mag_model(self, run_id_same_as, run_id):
"""
- Reset current magnetic metadata model for a given run id.
- Called when there is more than one run and selecting the "Same as run"
- option for run_id > a.
+ Reset current magnetic metadata model based on a user-selected run id.
+ Called when selecting the "Same as run" option for run_id > a.
"""
- self.submit_run_cha_md([run_id_same_as, run_id], mag_bool=True)
+ self.submit_run_cha_md(run_id_same_as, mag_bool=True)
self.check_before_reset(run_id_same_as, run_id, 'mag')
md = self.lemi_md.for_gui
key = f'Run_{run_id}_Mag'
@@ -527,7 +551,6 @@ class LemiWindow(*load_ui('mainwindow.ui')):
md_fields_s = self.sta_widgets.model
self.lemi_md.populate_sta_props(md_fields_s)
num_missing_invalid_s = self.flag_sta_md()
- self.num_missing_invalid_s = num_missing_invalid_s
return num_missing_invalid_s
def flag_run_md(self, run_list):
@@ -653,7 +676,7 @@ class LemiWindow(*load_ui('mainwindow.ui')):
"""
text = "Data and Metadata Conversion Status..."
details = ("All required metadata are properly filled out.\n"
- "You can now convert you data and metadata to an "
+ "You can now convert your data and metadata to an "
"archivable format!\nConsider saving the inputted "
"metadata (⌘S) before proceeding.")
icon = QtWidgets.QMessageBox.Information
diff --git a/lemi2seed/lemi2seed.py b/lemi2seed/lemi2seed.py
index fbf8479632d6b13f821c96130449f091949b3b88..0c30a796db60fe2f2c82fe78cad0e1e0cfaec4c6 100644
--- a/lemi2seed/lemi2seed.py
+++ b/lemi2seed/lemi2seed.py
@@ -41,16 +41,20 @@ lemi2seed can run under three distinct modes:
- gui only mode ('lemi2seed -d path2data -g)
- field sheet and gui mode (lemi2seed -d path2data -m path2metadata)
The 'quality control' mode allows to quickly convert LEMI data to mseed. The GUI and handling of metadata are bypassed.
-In the 'gui only' mode, metadata are entered only using the GUI.
-In the 'field sheet and gui' mode, metadata are prepopulated from parsing the provided field sheets.''')
+In the 'gui only' mode, metadata are entered/modified using only the GUI.
+In the 'field sheet and gui' mode, metadata are prepopulated from parsing the user-provided field sheets and modified using the GUI.''') # noqa: E501
parser.add_argument('-d',
dest='path2data',
metavar='path2data',
- help='''Path to the station where all folders/files generated by the LEMI-424 are stored''')
+ help='''Path to the station directory where all folders/files generated by the LEMI-424 are stored''') # noqa: E501
parser.add_argument('-m',
dest='path2md',
metavar='path2md',
- help='''Path to LEMI field spreadsheets''')
+ help='''Path to the directory where all LEMI field spreadsheets are stored''')
+ parser.add_argument('-s',
+ dest='path2savedmd',
+ metavar='path2savedmd',
+ help='''Path to the .pkl file where metadata were previously saved''')
parser.add_argument('-od',
dest='output_mseed',
metavar='output_mseed',
@@ -75,37 +79,36 @@ In the 'field sheet and gui' mode, metadata are prepopulated from parsing the pr
dest='gui_only_mode',
action='store_true',
default=False,
- help='''Runs lemi2seed in gui only mode. All metadata are entered using the GUI.
-Bypassing the use of field sheets.''')
+ help='''Runs lemi2seed in gui only mode. All metadata are entered using the GUI
+(bypassing the use of field sheets).''')
return parser
-def get_args() -> Tuple[Path, Optional[Path], bool, bool, Path, Path, Optional[Path]]:
- """
- Parse command line arguments and perform a serie of checks on command line
- arguments.
- """
- # Set up command line interface and parse command line arguments
- parser = setup_args()
- args = parser.parse_args()
-
- # Path to LEMI ASCII files
+def check_path2data(args: argparse.Namespace) -> Path:
+ """Check path to data files."""
if args.path2data and Path(args.path2data).is_dir():
path2data = Path(args.path2data).resolve()
else:
logger.error("Path to LEMI data not provided! Required input! "
"Try --help option.")
sys.exit(1)
+ return path2data
+
- # Running modes and path to LEMI field sheets
+def check_running_mode(args: argparse.Namespace) -> Tuple[bool, bool]:
+ """Check running mode selected by end-user."""
qc_only = args.qc_mode
gui_only = args.gui_only_mode
if all([qc_only, gui_only]):
logger.error("lemi2seed cannot run under both the 'quality control' "
- "and 'gui only' mode at the same time. Try --help option "
+ "and 'gui only' mode at the same time! Try --help option "
"or choose one or the other mode.")
sys.exit(1)
+ return qc_only, gui_only
+
+def check_path2metadata(args: argparse.Namespace, qc_only: bool, gui_only: bool) -> Optional[Path]:
+ """Check path to metadata file(s)."""
if args.path2md is None:
if not any([qc_only, gui_only]):
logger.error("No metadata path provided. Required input when "
@@ -116,13 +119,12 @@ def get_args() -> Tuple[Path, Optional[Path], bool, bool, Path, Path, Optional[P
else:
if Path(args.path2md).is_dir():
if qc_only:
- logger.info("Running lemi2seed in 'quality control' mode. "
- "Handling of metadata will be bypassed.")
+ logger.info("Handling of the field sheets is bypassed when "
+ "running in 'quality control' mode.")
path2md = None
elif gui_only:
- logger.info("Running lemi2seed in 'gui only' mode. All "
- "metadata should be entered using the GUI. "
- "Bypassing the use of field sheets.")
+ logger.info("All metadata should be entered using the GUI in "
+ "'gui only' mode. Bypassing the use of field sheets.")
path2md = None
else:
path2md = Path(args.path2md).resolve()
@@ -131,25 +133,38 @@ def get_args() -> Tuple[Path, Optional[Path], bool, bool, Path, Path, Optional[P
"exist!")
if any([qc_only, gui_only]):
logger.info("In 'quality control' or 'gui only' mode, field "
- "sheets are not parsed!")
+ "sheets are not parsed.")
path2md = None
else:
logger.error("A correct metadata path is a required input "
"when running in 'field sheet and gui' mode!")
sys.exit(1)
-
- # Output directories
- output_mseed = Path(args.output_mseed).resolve()
- check_output_dir(output_mseed, 'day-long mseed')
- output_log = Path(args.output_log).resolve()
- check_output_dir(output_log, 'log')
- if qc_only:
- output_xml = None
+ return path2md
+
+
+def check_path2savedmetadata(args: argparse.Namespace, qc_only: bool, gui_only: bool) -> Optional[Path]:
+ """Check path to saved metadata file(s)."""
+ if args.path2savedmd is not None:
+ if qc_only:
+ logger.info("Handling of previously saved metadata is bypassed when "
+ "running in 'quality control' mode.")
+ path2savedmd = None
+ elif gui_only:
+ if not Path(args.path2savedmd).is_file():
+ logger.error("The provided path to a previously saved metadata "
+ "file (*.pkl) does not exist! Bypassing loading "
+ "of metadata fields before launching the GUI.")
+ path2savedmd = None
+ else:
+ path2savedmd = Path(args.path2savedmd).resolve()
+ else:
+ logger.info("The loading of a previously saved metadata file (*.pkl) "
+ "is bypassed when running in 'field sheet and gui' "
+ "mode. Try --help option for more information.")
+ path2savedmd = None
else:
- output_xml = Path(args.output_xml).resolve()
- check_output_dir(output_xml, 'StationXML')
-
- return path2data, path2md, qc_only, gui_only, output_mseed, output_log, output_xml
+ path2savedmd = args.path2savedmd
+ return path2savedmd
def check_output_dir(output_dir: Path, output_type: str) -> None:
@@ -166,6 +181,36 @@ def check_output_dir(output_dir: Path, output_type: str) -> None:
sys.exit(1)
+def get_args() -> Tuple[Path, Optional[Path], Optional[Path], bool, bool, Path, Path, Optional[Path]]:
+ """
+ Parse command line arguments and perform a serie of checks on command line
+ arguments.
+ """
+ # Set up command line interface and parse command line arguments
+ parser = setup_args()
+ args = parser.parse_args()
+
+ # Check path to data directory, running modes, path to Phoenix field sheets
+ # and path to .pkl file
+ path2data = check_path2data(args)
+ qc_only, gui_only = check_running_mode(args)
+ path2md = check_path2metadata(args, qc_only, gui_only)
+ path2savedmd = check_path2savedmetadata(args, qc_only, gui_only)
+
+ # Check output directories
+ output_mseed = Path(args.output_mseed).resolve()
+ check_output_dir(output_mseed, 'day-long mseed')
+ output_log = Path(args.output_log).resolve()
+ check_output_dir(output_log, 'log')
+ if qc_only:
+ output_xml = None
+ else:
+ output_xml = Path(args.output_xml).resolve()
+ check_output_dir(output_xml, 'StationXML')
+
+ return path2data, path2md, path2savedmd, qc_only, gui_only, output_mseed, output_log, output_xml
+
+
def get_net_inputs() -> str:
"""Request user to enter 'network code'."""
while True:
@@ -319,7 +364,7 @@ def reformat_user_inputs(inputs: Dict) -> str:
return msg.strip("\n")
-def launch_gui(lemi_data: LemiData, lemi_md: LemiMetadata) -> None:
+def launch_gui(lemi_data: LemiData, lemi_md: LemiMetadata, path2savedmd: Path) -> None:
"""
Open GUI window, set the model data structure and handle metadata
processing and archival steps.
@@ -327,13 +372,15 @@ def launch_gui(lemi_data: LemiData, lemi_md: LemiMetadata) -> None:
"""
app = QtWidgets.QApplication(sys.argv)
lemi2seed_gui = LemiWindow(lemi_data, lemi_md)
+ if path2savedmd:
+ lemi2seed_gui.load_md(path2savedmd)
lemi2seed_gui.show()
sys.exit(app.exec_())
def main():
# Read command line arguments
- path2data, path2md, qc_only, gui_only, output_mseed, output_log, output_xml = get_args()
+ path2data, path2md, path2savedmd, qc_only, gui_only, output_mseed, output_log, output_xml = get_args()
# Parse data files
lemi_data = LemiData(path2data, output_mseed, output_log)
@@ -361,11 +408,13 @@ def main():
logger.info("Running lemi2seed in 'field sheet and gui' mode.")
md_fields = lemi_md.from_field_sheets
if md_fields is not None:
+ logger.info("Pre-populating the GUI metadata fields using the "
+ "information provided in the field sheet(s).")
lemi_md.populate_props(md_fields)
else:
logger.info("Running lemi2seed in 'gui only' mode.")
logger.info("Launching the GUI.")
- launch_gui(lemi_data, lemi_md)
+ launch_gui(lemi_data, lemi_md, path2savedmd)
if __name__ == '__main__':
diff --git a/lemi2seed/lemi_data.py b/lemi2seed/lemi_data.py
index 105420fcb820d7e37bc27464c8d5fc61e5414bb4..f20b586f3a2af7f0bf49cb0f209a8ac1e5448f30 100644
--- a/lemi2seed/lemi_data.py
+++ b/lemi2seed/lemi_data.py
@@ -14,6 +14,7 @@ import typing
from obspy import UTCDateTime
from pathlib import Path
+from statistics import mean
from typing import Dict, List, Optional, TYPE_CHECKING
from lemi2seed.logging import setup_logger
@@ -286,9 +287,9 @@ class LemiData():
These stats info are used to set the header information for a ObsPy
Trace object.
"""
- self.stats['lat'] = np.mean(self.data["Lat"])
- self.stats['lon'] = np.mean(self.data["Lon"])
- self.stats['elev'] = np.mean(self.data["Elev"])
+ self.stats['lat'] = mean(self.data["Lat"])
+ self.stats['lon'] = mean(self.data["Lon"])
+ self.stats['elev'] = mean(self.data["Elev"])
self.stats['start'] = self.data["Time_stamp"][0]
self.stats['end'] = self.data["Time_stamp"][-1]
diff --git a/lemi2seed/lemi_metadata.py b/lemi2seed/lemi_metadata.py
index 052b788ab3817322c9cfc1e5505701e7ae49f365..289ab57c9698e447a47814acb9ab0fb4397d4824 100644
--- a/lemi2seed/lemi_metadata.py
+++ b/lemi2seed/lemi_metadata.py
@@ -25,7 +25,7 @@ from typing import Dict, List, Optional, TYPE_CHECKING, Union
from lemi2seed.lemi_data import CHA_NAMING_CONV
from lemi2seed.logging import parse_config_ini, setup_logger
-from lemi2seed.metadata_category import Aux, Elec, Mag, Run, Sta, Net
+from lemi2seed.metadata_category import Aux, Elec, Mag, Run, Sta, Net, MSG_MAP
from lemi2seed.utils import (is_empty, eval_loc_code, get_e_loc, get_e_ids,
get_run_list, str2list, NUM_E_CHA_MAX)
@@ -222,19 +222,19 @@ class LemiMetadata():
output[cat] = LemiMetadata.dc2dict(mprop)
return output
- def parse_field_sheet(self, sheet: Worksheet, sheet_type: str, md_fields: Dict) -> Dict:
+ def parse_field_sheet(self, filename: Path, sheet: Worksheet, sheet_type: str, md_fields: Dict) -> Dict:
"""
Parse field sheet using the cell numbers listed in the config file and
return a nested dictionary of metadata entries organized based on the
category under which a given metadata field falls.
"""
- logger.info("Parsing the {} {}".format(*sheet_type.split('_')))
+ logger.info("Parsing the {} {} - {}.".format(*sheet_type.split('_'), filename))
for cat in self.cats[:-1]:
if cat not in md_fields:
md_fields[cat] = {}
if sheet_type not in config[cat]:
continue
- logger.info("Parsing '{}' metadata".format(cat))
+ logger.info("Parsing metadata fields at the {} level.".format(MSG_MAP[cat]))
for key, val in config[cat][sheet_type].items():
if isinstance(val, list):
field_val = [LemiMetadata.get_md_field(sheet, x) for x in val]
@@ -282,10 +282,24 @@ class LemiMetadata():
md_fields['Mag'] = self.reformat_mag(md_fields['Mag'])
return md_fields
+ @staticmethod
+ def check_field_sheets(sheet_types: List[Optional[str]]) -> None:
+ """
+ Check that all valid sheet types have been found and parsed. If not,
+ warn user of missing sheet(s).
+ """
+ valid_types = [key for key in config['sheets'].keys()[1:]]
+ for valid_type in valid_types:
+ if sheet_types and valid_type not in sheet_types:
+ logger.warning("No valid {0} sheet found. The {0} metadata "
+ "fields will have to be provided using the GUI."
+ .format(valid_type.split('_')[0]))
+
@property
def from_field_sheets(self) -> Optional[Dict]:
"""Parse all field sheets provided by the user."""
md_fields: Dict = {}
+ sheet_types = []
parsed_sheets = []
for filename in self.filenames:
try:
@@ -298,6 +312,7 @@ class LemiMetadata():
continue
sheet = workbook.active
sheet_type = self.identify_field_sheet(sheet, filename)
+ sheet_types.append(sheet_type)
if sheet_type is None:
continue
if sheet_type not in parsed_sheets:
@@ -307,8 +322,9 @@ class LemiMetadata():
"more than one {0} {1} - Skipping {2}!"
.format(*sheet_type.split('_'), filename))
continue
- md_fields = self.parse_field_sheet(sheet, sheet_type, md_fields)
+ md_fields = self.parse_field_sheet(filename, sheet, sheet_type, md_fields)
workbook.close()
+ LemiMetadata.check_field_sheets(sheet_types)
return self.reformat_md_dict(md_fields) if not is_empty(md_fields) else None
def populate(self, cat: DCS, md_fields: Dict, run_id: Optional[str] = None) -> None:
@@ -363,6 +379,23 @@ class LemiMetadata():
self.populate(self.net, md_fields_n)
LemiMetadata.flag_md_missing(self.net)
+ def check_sta_start_end(self) -> None:
+ """
+ Check that the start and end times of a station fall within the
+ network start and end times.
+ """
+ for time_field in ['start', 'end']:
+ time_net = getattr(self.net, time_field)
+ if time_field in self.sta.md_invalid or time_net is None:
+ continue
+ time_sta = getattr(self.sta, time_field)
+ valid = time_sta >= time_net if time_field == "start" else time_sta <= time_net
+ if not valid:
+ msg = "greater" if time_field == "start" else "lower"
+ logger.error("The {0} date of the station should be {1} than the {0} date "
+ "of the network.".format(time_field, msg))
+ self.sta.md_invalid.add(time_field)
+
def populate_sta_props(self, md_fields_s: Dict) -> None:
"""
Populate properties of Sta data class based on user inputs from
@@ -370,6 +403,7 @@ class LemiMetadata():
"""
self.populate(self.sta, md_fields_s)
self.sta.run_list = ', '.join(self.run_list)
+ self.check_sta_start_end()
LemiMetadata.flag_md_missing(self.sta)
def get_run(self, run_id: str) -> Run:
@@ -391,20 +425,13 @@ class LemiMetadata():
self.populate(run, md_fields_r[name], run_id)
LemiMetadata.flag_md_missing(run)
- def get_comps_rec(self, type_: str, run_id: str, msg: Optional[bool] = True) -> list:
+ def get_comps_rec(self, type_: str, run_id: str) -> list:
"""
For a given channel type (electric or magnetic) and a given run_id,
get components recorded.
"""
run = self.get_run(run_id)
- cha_type = 'electric field' if type_ == 'E' else 'magnetic field'
if run.comps_rec is None:
- if msg:
- logger.warning("No set of recorded components found for run "
- "'{0}'. If you did record {1} data for that run, "
- "please update the 'components recorded' "
- "metadata field at the Station/Runs level!"
- .format(run_id, cha_type))
return []
else:
comps = [x for x in str2list(run.comps_rec, sep='-') if x.startswith(type_)] # type: ignore
@@ -436,7 +463,7 @@ class LemiMetadata():
e_infos = {}
for run in self.run:
run_id = run.run_id
- e_pairs = self.get_comps_rec('E', run_id, msg=False)
+ e_pairs = self.get_comps_rec('E', run_id)
elec = self.filter_cha('elec', run_id)
e_infos[run_id] = {x.cha_port: x.comp for x in elec if f'E{x.pair_num}' in e_pairs} # type: ignore
return e_infos
diff --git a/lemi2seed/lemi_response.py b/lemi2seed/lemi_response.py
index 298f7d667f0bc90c421511391ea96e98df052468..a967f073ab7d56b952c4b8659f603b69ba62800d 100644
--- a/lemi2seed/lemi_response.py
+++ b/lemi2seed/lemi_response.py
@@ -66,18 +66,18 @@ logger = setup_logger(__name__)
RESP_FILE = Path(__file__).resolve().parent.joinpath('response_file', 'LEMI-424_Response')
SOH_STAGE_GAIN = 1.0
SOH_STAGE_GAIN_FREQUENCY = 0.0
-CHA_UNITS = {'E1': ['microvolt per meter', 'electric field units'],
- 'E2': ['microvolt per meter', 'electric field units'],
- 'E3': ['microvolt per meter', 'electric field units'],
- 'E4': ['microvolt per meter', 'electric field units'],
+CHA_UNITS = {'E1': ['uV/m', 'electric field units'],
+ 'E2': ['uV/m', 'electric field units'],
+ 'E3': ['uV/m', 'electric field units'],
+ 'E4': ['uV/m', 'electric field units'],
'Hx': ['nanotesla', 'magnetic field units'],
'Hy': ['nanotesla', 'magnetic field units'],
'Hz': ['nanotesla', 'magnetic field units'],
'Ui': ['V', 'electric potential in volts'],
'Te': ['celsius', 'temperature in degrees Celsius'],
'Tf': ['celsius', 'temperature in degrees Celsius'],
- 'Sn': ['', 'unitless'],
- 'Fq': ['', 'unitless'],
+ 'Sn': ['unitless', 'unitless'],
+ 'Fq': ['unitless', 'unitless'],
'Ce': ['s', 'second']}
diff --git a/lemi2seed/metadata_category.py b/lemi2seed/metadata_category.py
index eda89880dc37952fc5560aaaf273777e1573ed5e..9cffc84eb75774bd1e99897de4b4a14f55aaee45 100644
--- a/lemi2seed/metadata_category.py
+++ b/lemi2seed/metadata_category.py
@@ -19,9 +19,8 @@ from typing import Dict, Optional, Set
from lemi2seed.lemi_data import SAMPLING_RATE, CHA_NAMING_CONV
from lemi2seed.logging import parse_config_ini, setup_logger
-from lemi2seed.utils import (check_email_format, check_inst_specs, check_sn,
- is_valid_uri, str2list, ELEC_DEFAULT,
- FLUXGATE_DEFAULT)
+from lemi2seed.utils import (check_inst_specs, check_sn, str2list,
+ ELEC_DEFAULT, FLUXGATE_DEFAULT)
# Read config.ini file and set up logging
config = parse_config_ini()
@@ -32,9 +31,10 @@ logger = setup_logger(__name__)
CLOCKDRIFT = 1.0
E_COMP_NAMING_CONV = {'North-South': 'Ex', 'South-North': 'Ex',
'East-West': 'Ey', 'West-East': 'Ey'}
-MAXIMUM_AZIMUTH = 99999
-MINIMUM_AZIMUTH = -99999
-MSG_MAP = {'Net': 'network', 'Sta': 'station'}
+MAXIMUM_GEO = 99999
+MINIMUM_GEO = -99999
+MSG_MAP = {'Net': 'network', 'Sta': 'station', 'Run': 'run', 'Elec': 'electric',
+ 'Mag': 'magnetic'}
VALID_COMPS = ['Hx - Hy - Hz', 'E1 - E2 - Hx - Hy - Hz', 'E1 - E2 - E3 - E4 - Hx - Hy - Hz']
@@ -57,9 +57,6 @@ class BaseNet(BaseMD):
This class handles the metadata attributes shared at the network and station
levels.
"""
- restricted_status: Optional[str] = field(default=None,
- metadata={'xml_id': ['restricted_status'],
- 'req': False, 'gui': True})
end: Optional[UTCDateTime] = field(default=None,
metadata={'xml_id': ['end_date'],
'req': True, 'gui': True})
@@ -97,9 +94,6 @@ class Net(BaseNet):
'req': False, 'gui': True})
archive_net: Optional[str] = field(default=None,
metadata={'req': True, 'gui': True})
- citation_dataset_doi: Optional[str] = field(default=None,
- metadata={'xml_id': ['identifiers'],
- 'req': False, 'gui': True})
comments: Optional[str] = field(default=None,
metadata={'xml_id': ['comments', 'mt.network.comments'],
'req': False, 'gui': True})
@@ -118,9 +112,6 @@ class Net(BaseNet):
project_lead_author: Optional[str] = field(default=None,
metadata={'xml_id': ['operators.contacts.names'],
'req': False, 'gui': True})
- project_lead_email: Optional[str] = field(default=None,
- metadata={'xml_id': ['operators.contacts.emails'],
- 'req': False, 'gui': True})
project_lead_organization: Optional[str] = field(default=None,
metadata={'xml_id': ['operators.agency'],
'req': False, 'gui': True})
@@ -141,37 +132,6 @@ class Net(BaseNet):
"character long.")
return bool(valid)
- @staticmethod
- def validate_citation_dataset_doi(md_input: str) -> bool:
- """
- Proper formatting for DOI?
- """
- if md_input is not None:
- try:
- dois = str2list(md_input)
- except AttributeError:
- logger.error('The DOI number(s) should be a string.')
- return False
- else:
- if not all([is_valid_uri(doi) for doi in dois]):
- logger.error("Invalid DOI(s). The DOI number(s) provided by "
- "the archive should be strings formatted as "
- "follows: 'scheme: path'.")
- return False
- return True
- return True
-
- @staticmethod
- def validate_project_lead_email(md_input: str) -> bool:
- if md_input is not None:
- try:
- emails = str2list(md_input)
- except AttributeError:
- logger.error('The project lead email(s) should be a string.')
- return False
- return all([check_email_format(email) for email in emails])
- return True
-
@dataclass
class BaseSta(BaseMD):
@@ -203,11 +163,12 @@ class BaseSta(BaseMD):
"{3} and {2}{3}.".format(geo, min_range,
max_range, units))
return False
- elif md_input < min_val or md_input > max_val:
- logger.error("Unexpected {0}! Provided {0} should "
- "roughly match the {0} recorded by the on-site "
- "GPS ({1:.3f}{2}).".format(geo, val, units))
- return False
+ if md_input < min_val or md_input > max_val:
+ tolerance = max_val - val
+ logger.warning("Unexpected {0}! Provided {0} should "
+ "roughly match the {0} recorded by the on-site "
+ "GPS ({1:.3f} ± {2:.3f}{3})."
+ .format(geo, val, tolerance, units))
return True
def validate_elev(self, md_input: float, data_input: float) -> bool:
@@ -264,9 +225,6 @@ class Sta(BaseNet, BaseSta):
submitter_author: Optional[str] = field(default=None,
metadata={'xml_id': ['comments', 'mt.station.provenance.submitter.author'],
'req': False, 'gui': True})
- submitter_email: Optional[str] = field(default=None,
- metadata={'xml_id': ['comments', 'mt.station.provenance.submitter.email'],
- 'req': False, 'gui': True})
submitter_organization: Optional[str] = field(default=None,
metadata={'xml_id': ['comments', 'mt.station.provenance.submitter.organization'], # noqa: E501
'req': False, 'gui': True})
@@ -285,15 +243,9 @@ class Sta(BaseNet, BaseSta):
return bool(valid)
def validate_declination_val(self, md_input: float) -> bool:
- param = ("declination angle", -90, 90, MINIMUM_AZIMUTH, MAXIMUM_AZIMUTH, None, '°')
+ param = ("declination angle", -90, 90, MINIMUM_GEO, MAXIMUM_GEO, None, '°')
return BaseSta.validate_geos(param, md_input)
- @staticmethod
- def validate_submitter_email(md_input: str) -> bool:
- if md_input is not None:
- return check_email_format(md_input)
- return True
-
@dataclass
class Run(BaseMD):
@@ -358,8 +310,8 @@ class Run(BaseMD):
comps = str2list(md_input, sep='-') if '-' in md_input else str2list(md_input)
except (AttributeError, TypeError):
- logger.error("The list of components recorded for run '{}' "
- "should be a string. Example: {}"
+ logger.error("The 'components recorded' metadata field is empty "
+ "for run '{}'. Example of valid field: {}"
.format(self.run_id, VALID_COMPS[0]))
return False
else:
@@ -421,7 +373,7 @@ class BaseChannel(BaseSta):
geo = "azimuth angle of electrode pair {0} (run '{1}')".format(self.pair_num, self.run_id)
if isinstance(self, Mag):
geo = "azimuth angle of fluxgate (run '{}')".format(self.run_id)
- param = (geo, 0, 360, MINIMUM_AZIMUTH, MAXIMUM_AZIMUTH, None, '°')
+ param = (geo, 0, 360, MINIMUM_GEO, MAXIMUM_GEO, None, '°')
return BaseSta.validate_geos(param, md_input)
def validate_meas_tilt(self, md_input: float) -> bool:
@@ -429,7 +381,7 @@ class BaseChannel(BaseSta):
geo = "tilt angle of electrode pair {0} (run '{1}')".format(self.pair_num, self.run_id)
if isinstance(self, Mag):
geo = "tilt angle of fluxgate (run '{}')".format(self.run_id)
- param = (geo, -90, 90, MINIMUM_AZIMUTH, MAXIMUM_AZIMUTH, None, '°')
+ param = (geo, -90, 90, MINIMUM_GEO, MAXIMUM_GEO, None, '°')
return BaseSta.validate_geos(param, md_input)
diff --git a/lemi2seed/metadata_conversion.py b/lemi2seed/metadata_conversion.py
index 864441c0a3e5b0494ff3fbc7ed5514ebf31eaaef..fdbdeae2879bf4fbfc17f67fe43aa8cf7e09d102 100644
--- a/lemi2seed/metadata_conversion.py
+++ b/lemi2seed/metadata_conversion.py
@@ -81,11 +81,12 @@ def create_net(net: Net) -> Network:
comments.append(comment)
elif 'operators' in net_field_info[0]:
if 'agency' in net_field_info[0]:
+ # Address agency related change in StationXML 1.1
+ if not net_field_val:
+ net_field_val = ' '
operator = Operator(agency=net_field_val)
- elif 'names' in net_field_info[0]:
- person.names = str2list(net_field_val)
else:
- person.emails = str2list(net_field_val)
+ person.names = str2list(net_field_val)
elif net_field_info[0] == 'identifiers':
net_.identifiers = str2list(net_field_val)
else:
@@ -414,6 +415,7 @@ def write_stationxml(lemi_md: LemiMetadata) -> None:
filename = '.'.join([lemi_md.data_stats['net'], lemi_md.data_stats['sta'],
'_'.join([x.upper() for x in lemi_md.net.project.split(" ")]), # type: ignore
UTCDateTime().strftime('%Y%j.%H%M%S'), 'xml'])
+ filename = str(lemi_md.output_xml.joinpath(filename))
logger.info("Writing StationXML file: {}.".format(filename))
inv = create_inventory()
net = create_net(lemi_md.net)
@@ -426,5 +428,5 @@ def write_stationxml(lemi_md: LemiMetadata) -> None:
sta.equipments = loggers
net.stations = [sta]
inv.networks = [net]
- inv.write(str(lemi_md.output_xml.joinpath(filename)), format="STATIONXML")
+ inv.write(filename, format="STATIONXML")
logger.info("Writing of StationXML file successfully completed!")
diff --git a/lemi2seed/ui_files/electricwidget.ui b/lemi2seed/ui_files/electricwidget.ui
index 92192e5fdac005497d244012337a7d2ad330ba6b..bc45f7f934df60960b9f4bbd681a380ad018e854 100644
--- a/lemi2seed/ui_files/electricwidget.ui
+++ b/lemi2seed/ui_files/electricwidget.ui
@@ -235,7 +235,7 @@ Set to 1 Hz since the LEMI datalogger only has one sample rate for data recordin
</font>
</property>
<property name="text">
- <string>Negative Electrode</string>
+ <string>Positive Electrode</string>
</property>
</widget>
</item>
@@ -251,7 +251,7 @@ By convention South or West.</string>
</widget>
</item>
<item row="13" column="1">
- <widget class="QComboBox" name="uiNegElecDir">
+ <widget class="QComboBox" name="uiPosElecDir">
<property name="sizePolicy">
<sizepolicy hsizetype="Expanding" vsizetype="Fixed">
<horstretch>0</horstretch>
@@ -294,7 +294,7 @@ By convention South or West.</string>
</widget>
</item>
<item row="14" column="1">
- <widget class="QLineEdit" name="uiNegElecSn"/>
+ <widget class="QLineEdit" name="uiPosElecSn"/>
</item>
<item row="15" column="0">
<widget class="QLabel" name="label_11">
@@ -304,7 +304,7 @@ By convention South or West.</string>
</font>
</property>
<property name="text">
- <string>Positive Electrode</string>
+ <string>Negative Electrode</string>
</property>
</widget>
</item>
@@ -320,7 +320,7 @@ By convention North or East.</string>
</widget>
</item>
<item row="16" column="1">
- <widget class="QComboBox" name="uiPosElecDir">
+ <widget class="QComboBox" name="uiNegElecDir">
<property name="sizePolicy">
<sizepolicy hsizetype="Expanding" vsizetype="Fixed">
<horstretch>0</horstretch>
@@ -363,7 +363,7 @@ By convention North or East.</string>
</widget>
</item>
<item row="17" column="1">
- <widget class="QLineEdit" name="uiPosElecSn"/>
+ <widget class="QLineEdit" name="uiNegElecSn"/>
</item>
</layout>
</widget>
diff --git a/lemi2seed/ui_files/helpwidget.ui b/lemi2seed/ui_files/helpwidget.ui
index 2250cbd00d14a1b2cde0dfeccced8aefb29da537..358d7e269a9a4288aac70e7ef17bb17f01a29906 100644
--- a/lemi2seed/ui_files/helpwidget.ui
+++ b/lemi2seed/ui_files/helpwidget.ui
@@ -6,10 +6,16 @@
<rect>
<x>0</x>
<y>0</y>
- <width>1091</width>
- <height>438</height>
+ <width>1200</width>
+ <height>721</height>
</rect>
</property>
+ <property name="minimumSize">
+ <size>
+ <width>1100</width>
+ <height>600</height>
+ </size>
+ </property>
<property name="windowTitle">
<string>Form</string>
</property>
@@ -21,8 +27,8 @@
<rect>
<x>10</x>
<y>10</y>
- <width>1111</width>
- <height>91</height>
+ <width>1130</width>
+ <height>100</height>
</rect>
</property>
<property name="styleSheet">
@@ -33,11 +39,11 @@
<html><head><meta name="qrichtext" content="1" /><style type="text/css">
p, li { white-space: pre-wrap; }
</style></head><body style=" font-family:'.AppleSystemUIFont'; font-size:13pt; font-weight:400; font-style:normal;">
-<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">Description</span></p>
-<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">lemi2seed is a GUI software tool developped by the PASSCAL Instrument Center to convert LEMI data and metadata into day-long mseed and StationXML files.</p>
-<p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /></p>
-<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">Usage</span></p>
-<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The tool bar offers the following options:</p></body></html></string>
+<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-size:15pt; font-weight:600;">Description</span></p>
+<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-size:15pt;">lemi2seed is a GUI software tool developped by the PASSCAL Instrument Center to convert LEMI data and metadata into day-long mseed and StationXML files.</span></p>
+<p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-size:15pt;"><br /></p>
+<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-size:15pt; font-weight:600;">Usage</span></p>
+<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-size:15pt;">The tool bar offers the following options:</span></p></body></html></string>
</property>
<property name="textInteractionFlags">
<set>Qt::NoTextInteraction</set>
@@ -47,9 +53,9 @@ p, li { white-space: pre-wrap; }
<property name="geometry">
<rect>
<x>20</x>
- <y>110</y>
- <width>25</width>
- <height>25</height>
+ <y>130</y>
+ <width>30</width>
+ <height>30</height>
</rect>
</property>
<property name="styleSheet">
@@ -63,9 +69,9 @@ p, li { white-space: pre-wrap; }
<property name="geometry">
<rect>
<x>60</x>
- <y>110</y>
- <width>731</width>
- <height>31</height>
+ <y>130</y>
+ <width>1080</width>
+ <height>30</height>
</rect>
</property>
<property name="styleSheet">
@@ -76,7 +82,7 @@ p, li { white-space: pre-wrap; }
<html><head><meta name="qrichtext" content="1" /><style type="text/css">
p, li { white-space: pre-wrap; }
</style></head><body style=" font-family:'.AppleSystemUIFont'; font-size:13pt; font-weight:400; font-style:normal;">
-<p align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Upload metadata previously saved with the GUI. The uploaded file has to be in a pickle format (.pkl file extension).</p></body></html></string>
+<p align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-size:15pt;">Upload metadata previously saved with the GUI. The uploaded file has to be in a pickle format (.pkl file extension).</span></p></body></html></string>
</property>
<property name="textInteractionFlags">
<set>Qt::NoTextInteraction</set>
@@ -86,9 +92,9 @@ p, li { white-space: pre-wrap; }
<property name="geometry">
<rect>
<x>20</x>
- <y>144</y>
- <width>25</width>
- <height>25</height>
+ <y>180</y>
+ <width>30</width>
+ <height>30</height>
</rect>
</property>
<property name="styleSheet">
@@ -102,9 +108,9 @@ p, li { white-space: pre-wrap; }
<property name="geometry">
<rect>
<x>60</x>
- <y>140</y>
- <width>681</width>
- <height>31</height>
+ <y>182</y>
+ <width>1081</width>
+ <height>30</height>
</rect>
</property>
<property name="styleSheet">
@@ -115,7 +121,7 @@ p, li { white-space: pre-wrap; }
<html><head><meta name="qrichtext" content="1" /><style type="text/css">
p, li { white-space: pre-wrap; }
</style></head><body style=" font-family:'.AppleSystemUIFont'; font-size:13pt; font-weight:400; font-style:normal;">
-<p align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Save inputted metadata. The metadata will be stored in a pickle format (.pkl file extension).</p></body></html></string>
+<p align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-size:15pt;">Save inputted metadata. The metadata will be stored in a pickle format (.pkl file extension).</span></p></body></html></string>
</property>
<property name="textInteractionFlags">
<set>Qt::NoTextInteraction</set>
@@ -125,9 +131,9 @@ p, li { white-space: pre-wrap; }
<property name="geometry">
<rect>
<x>20</x>
- <y>185</y>
- <width>28</width>
- <height>28</height>
+ <y>240</y>
+ <width>34</width>
+ <height>34</height>
</rect>
</property>
<property name="styleSheet">
@@ -141,9 +147,9 @@ p, li { white-space: pre-wrap; }
<property name="geometry">
<rect>
<x>60</x>
- <y>170</y>
- <width>1051</width>
- <height>61</height>
+ <y>220</y>
+ <width>1080</width>
+ <height>80</height>
</rect>
</property>
<property name="styleSheet">
@@ -154,9 +160,9 @@ p, li { white-space: pre-wrap; }
<html><head><meta name="qrichtext" content="1" /><style type="text/css">
p, li { white-space: pre-wrap; }
</style></head><body style=" font-family:'.AppleSystemUIFont'; font-size:13pt; font-weight:400; font-style:normal;">
-<p align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Write day-long mseed files in user defined output directory or default directory (./MSEED).</p>
-<p align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Write calibration information in log file under user defined output directory or default directory (./LOGS) if calibration coefficient files (.def) were provided by the user. </p>
-<p align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">This option is only enabled if all user provided metadata are valid and all required metadata are filled.</p></body></html></string>
+<p align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-size:15pt;">Write day-long mseed files in user defined output directory or default directory (./MSEED).</span></p>
+<p align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-size:15pt;">Write calibration information in log file under user defined output directory or default directory (./LOGS) if calibration coefficient files (.def) were provided by the user. </span></p>
+<p align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-size:15pt;">This option is only enabled if all user provided metadata are valid and all required metadata are filled.</span></p></body></html></string>
</property>
<property name="textInteractionFlags">
<set>Qt::NoTextInteraction</set>
@@ -166,9 +172,9 @@ p, li { white-space: pre-wrap; }
<property name="geometry">
<rect>
<x>20</x>
- <y>238</y>
- <width>25</width>
- <height>25</height>
+ <y>315</y>
+ <width>30</width>
+ <height>30</height>
</rect>
</property>
<property name="styleSheet">
@@ -182,9 +188,9 @@ p, li { white-space: pre-wrap; }
<property name="geometry">
<rect>
<x>60</x>
- <y>230</y>
- <width>681</width>
- <height>41</height>
+ <y>310</y>
+ <width>1080</width>
+ <height>50</height>
</rect>
</property>
<property name="styleSheet">
@@ -195,8 +201,8 @@ p, li { white-space: pre-wrap; }
<html><head><meta name="qrichtext" content="1" /><style type="text/css">
p, li { white-space: pre-wrap; }
</style></head><body style=" font-family:'.AppleSystemUIFont'; font-size:13pt; font-weight:400; font-style:normal;">
-<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Write StationXML file in user defined output directory or default directory (./STATIONXML).</p>
-<p align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">This option will only be enabled if all user provided metadata are valid and all required metadata are filled.</p></body></html></string>
+<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-size:15pt;">Write StationXML file in user defined output directory or default directory (./STATIONXML).</span></p>
+<p align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-size:15pt;">This option will only be enabled if all user provided metadata are valid and all required metadata are filled.</span></p></body></html></string>
</property>
<property name="textInteractionFlags">
<set>Qt::NoTextInteraction</set>
@@ -206,9 +212,9 @@ p, li { white-space: pre-wrap; }
<property name="geometry">
<rect>
<x>10</x>
- <y>290</y>
- <width>1061</width>
- <height>151</height>
+ <y>370</y>
+ <width>1130</width>
+ <height>160</height>
</rect>
</property>
<property name="styleSheet">
@@ -219,14 +225,14 @@ p, li { white-space: pre-wrap; }
<html><head><meta name="qrichtext" content="1" /><style type="text/css">
p, li { white-space: pre-wrap; }
</style></head><body style=" font-family:'.AppleSystemUIFont'; font-size:13pt; font-weight:400; font-style:normal;">
-<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The main window has four panels: <span style=" font-weight:600;">Network</span>, <span style=" font-weight:600;">Station</span>, <span style=" font-weight:600;">Electric</span>, <span style=" font-weight:600;">Magnetic</span>. To navigate from one panel to another, just select the panel of interest.</p>
-<p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /></p>
-<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">In each panel, the required metadata are identified with the asterisk symbol (<span style=" font-weight:600;">*</span>).</p>
-<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">For more information about a metadata field and its expected format, hover your mouse on its label.</p>
-<p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /></p>
-<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">To validate the inputted metadata, select the &quot;<span style=" font-weight:600;">Validate Metadata</span>&quot; button in the bottom right corner of the main window.</p>
-<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Invalid metadata or unfilled required metadata will be circled in red. The name of the panels for which metadata are invalid or missing will also be highlighted in red.</p>
-<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">For more information about why a given metadata field is flagged as invalid, check the logging outputs in the terminal window.</p></body></html></string>
+<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-size:15pt;">The main window has four panels: </span><span style=" font-size:15pt; font-weight:600;">Network</span><span style=" font-size:15pt;">, </span><span style=" font-size:15pt; font-weight:600;">Station</span><span style=" font-size:15pt;">, </span><span style=" font-size:15pt; font-weight:600;">Electric</span><span style=" font-size:15pt;">, </span><span style=" font-size:15pt; font-weight:600;">Magnetic</span><span style=" font-size:15pt;">. To navigate from one panel to another, just select the panel of interest.</span></p>
+<p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-size:15pt;"><br /></p>
+<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-size:15pt;">In each panel, the required metadata are identified with the asterisk symbol (</span><span style=" font-size:15pt; font-weight:600;">*</span><span style=" font-size:15pt;">).</span></p>
+<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-size:15pt;">For more information about a metadata field and its expected format, hover your mouse on its label.</span></p>
+<p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-size:15pt;"><br /></p>
+<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-size:15pt;">To validate the inputted metadata, select the &quot;</span><span style=" font-size:15pt; font-weight:600;">Validate Metadata</span><span style=" font-size:15pt;">&quot; button in the bottom right corner of the main window.</span></p>
+<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-size:15pt;">Invalid metadata or unfilled required metadata will be circled in red. The name of the panels for which metadata are invalid or missing will also be highlighted in red.</span></p>
+<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-size:15pt;">For more information about why a given metadata field is flagged as invalid, check the logging outputs in the terminal window.</span></p></body></html></string>
</property>
<property name="textInteractionFlags">
<set>Qt::NoTextInteraction</set>
diff --git a/lemi2seed/ui_files/magneticwidget.ui b/lemi2seed/ui_files/magneticwidget.ui
index 5a4f35335d5e8a5cca603b5c47f78e6f440c63ba..86213fd2287cb16e195c95b32e0e469a92935e2d 100644
--- a/lemi2seed/ui_files/magneticwidget.ui
+++ b/lemi2seed/ui_files/magneticwidget.ui
@@ -81,10 +81,10 @@ If the fluxgate is installed perfectly vertically, the provided tilt angle shoul
<item row="3" column="0">
<widget class="QLabel" name="label_4">
<property name="toolTip">
- <string>Magnetometer specifications (Manufacturer - Model - Type).</string>
+ <string>Fluxgate specifications (Manufacturer - Model - Type).</string>
</property>
<property name="text">
- <string>Magnetometer - Specs *</string>
+ <string>Fluxgate - Specs *</string>
</property>
</widget>
</item>
@@ -108,10 +108,10 @@ If the fluxgate is installed perfectly vertically, the provided tilt angle shoul
<item row="4" column="0">
<widget class="QLabel" name="label_5">
<property name="toolTip">
- <string>Serial number of magnetometer.</string>
+ <string>Serial number of fluxgate.</string>
</property>
<property name="text">
- <string>Magnetometer - Serial Number *</string>
+ <string>Fluxgate - Serial Number *</string>
</property>
</widget>
</item>
diff --git a/lemi2seed/ui_files/networkwidget.ui b/lemi2seed/ui_files/networkwidget.ui
index e4c69966bb26022cd1761a29a076ad4fed257da6..c797e6e5682f02fe6451ceeceb10e99d68af295b 100644
--- a/lemi2seed/ui_files/networkwidget.ui
+++ b/lemi2seed/ui_files/networkwidget.ui
@@ -106,16 +106,23 @@ Should be two characters long.</string>
</property>
<property name="date">
<date>
- <year>2021</year>
- <month>1</month>
- <day>1</day>
+ <year>1999</year>
+ <month>12</month>
+ <day>31</day>
</date>
</property>
+ <property name="time">
+ <time>
+ <hour>17</hour>
+ <minute>0</minute>
+ <second>0</second>
+ </time>
+ </property>
<property name="currentSection">
<enum>QDateTimeEdit::YearSection</enum>
</property>
<property name="displayFormat">
- <string>yyyy-MM-dd</string>
+ <string>yyyy-MM-dd HH:mm:ss</string>
</property>
<property name="calendarPopup">
<bool>true</bool>
@@ -157,16 +164,23 @@ Should be two characters long.</string>
</property>
<property name="date">
<date>
- <year>2021</year>
- <month>1</month>
- <day>1</day>
+ <year>2999</year>
+ <month>12</month>
+ <day>31</day>
</date>
</property>
+ <property name="time">
+ <time>
+ <hour>16</hour>
+ <minute>59</minute>
+ <second>59</second>
+ </time>
+ </property>
<property name="currentSection">
<enum>QDateTimeEdit::YearSection</enum>
</property>
<property name="displayFormat">
- <string>yyyy-MM-dd</string>
+ <string>yyyy-MM-dd HH:mm:ss</string>
</property>
<property name="calendarPopup">
<bool>true</bool>
@@ -177,56 +191,6 @@ Should be two characters long.</string>
</widget>
</item>
<item row="3" column="0">
- <widget class="QLabel" name="label_5">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Preferred">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="toolTip">
- <string>Are the access to the data at the network level open, partially open or closed?</string>
- </property>
- <property name="text">
- <string>Restricted status</string>
- </property>
- </widget>
- </item>
- <item row="3" column="1">
- <widget class="QComboBox" name="uiRestrictedStatus">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="font">
- <font>
- <weight>50</weight>
- <bold>false</bold>
- </font>
- </property>
- <property name="focusPolicy">
- <enum>Qt::StrongFocus</enum>
- </property>
- <item>
- <property name="text">
- <string>open</string>
- </property>
- </item>
- <item>
- <property name="text">
- <string>partial</string>
- </property>
- </item>
- <item>
- <property name="text">
- <string>closed</string>
- </property>
- </item>
- </widget>
- </item>
- <item row="4" column="0">
<widget class="QLabel" name="label_4">
<property name="sizePolicy">
<sizepolicy hsizetype="Preferred" vsizetype="Preferred">
@@ -251,7 +215,7 @@ Should be two characters long.</string>
</property>
</widget>
</item>
- <item row="4" column="1">
+ <item row="3" column="1">
<widget class="QPlainTextEdit" name="uiComments">
<property name="sizePolicy">
<sizepolicy hsizetype="Expanding" vsizetype="Expanding">
@@ -328,34 +292,6 @@ Should be two characters long.</string>
<widget class="QLineEdit" name="uiAcqByComments"/>
</item>
<item row="2" column="0">
- <widget class="QLabel" name="label_7">
- <property name="font">
- <font>
- <weight>50</weight>
- <bold>false</bold>
- </font>
- </property>
- <property name="toolTip">
- <string>DOI number provided by the archive.
-Ex: DOI:10.17611/DP/EMTF/USGS/GEOMAG/FL15.
-If multiple, input as comma separated. </string>
- </property>
- <property name="text">
- <string>Digital Object Identifier(s)</string>
- </property>
- </widget>
- </item>
- <item row="2" column="1">
- <widget class="QLineEdit" name="uiCitationDatasetDoi">
- <property name="font">
- <font>
- <weight>50</weight>
- <bold>false</bold>
- </font>
- </property>
- </widget>
- </item>
- <item row="3" column="0">
<widget class="QLabel" name="label_8">
<property name="font">
<font>
@@ -373,7 +309,7 @@ Ex: USA, Canada</string>
</property>
</widget>
</item>
- <item row="3" column="1">
+ <item row="2" column="1">
<widget class="QLineEdit" name="uiCountry">
<property name="font">
<font>
@@ -383,7 +319,7 @@ Ex: USA, Canada</string>
</property>
</widget>
</item>
- <item row="4" column="0">
+ <item row="3" column="0">
<widget class="QLabel" name="label_9">
<property name="font">
<font>
@@ -401,7 +337,7 @@ Ex: Eastern Mojave, Southwestern USA</string>
</property>
</widget>
</item>
- <item row="4" column="1">
+ <item row="3" column="1">
<widget class="QLineEdit" name="uiGeoName">
<property name="font">
<font>
@@ -411,7 +347,7 @@ Ex: Eastern Mojave, Southwestern USA</string>
</property>
</widget>
</item>
- <item row="5" column="0">
+ <item row="4" column="0">
<widget class="QLabel" name="label_10">
<property name="font">
<font>
@@ -428,7 +364,7 @@ Ex: MT Characterization of Yukon Terrane</string>
</property>
</widget>
</item>
- <item row="5" column="1">
+ <item row="4" column="1">
<widget class="QLineEdit" name="uiName">
<property name="font">
<font>
@@ -438,7 +374,7 @@ Ex: MT Characterization of Yukon Terrane</string>
</property>
</widget>
</item>
- <item row="6" column="0">
+ <item row="5" column="0">
<widget class="QLabel" name="label_11">
<property name="font">
<font>
@@ -457,7 +393,7 @@ Ex: GEOMAG</string>
</property>
</widget>
</item>
- <item row="6" column="1">
+ <item row="5" column="1">
<widget class="QLineEdit" name="uiProject">
<property name="font">
<font>
@@ -467,7 +403,7 @@ Ex: GEOMAG</string>
</property>
</widget>
</item>
- <item row="7" column="0">
+ <item row="6" column="0">
<widget class="QLabel" name="label_12">
<property name="font">
<font>
@@ -485,7 +421,7 @@ If multiple, input as comma separated.</string>
</property>
</widget>
</item>
- <item row="7" column="1">
+ <item row="6" column="1">
<widget class="QLineEdit" name="uiProjectLeadAuthor">
<property name="font">
<font>
@@ -495,34 +431,7 @@ If multiple, input as comma separated.</string>
</property>
</widget>
</item>
- <item row="8" column="0">
- <widget class="QLabel" name="label_13">
- <property name="font">
- <font>
- <weight>50</weight>
- <bold>false</bold>
- </font>
- </property>
- <property name="toolTip">
- <string>Email of the project lead.
-If multiple, input as comma separated.</string>
- </property>
- <property name="text">
- <string>Project Lead - Email(s)</string>
- </property>
- </widget>
- </item>
- <item row="8" column="1">
- <widget class="QLineEdit" name="uiProjectLeadEmail">
- <property name="font">
- <font>
- <weight>50</weight>
- <bold>false</bold>
- </font>
- </property>
- </widget>
- </item>
- <item row="9" column="0">
+ <item row="7" column="0">
<widget class="QLabel" name="label_14">
<property name="font">
<font>
@@ -538,7 +447,7 @@ If multiple, input as comma separated.</string>
</property>
</widget>
</item>
- <item row="9" column="1">
+ <item row="7" column="1">
<widget class="QLineEdit" name="uiProjectLeadOrganization">
<property name="font">
<font>
@@ -548,7 +457,7 @@ If multiple, input as comma separated.</string>
</property>
</widget>
</item>
- <item row="10" column="0">
+ <item row="8" column="0">
<widget class="QLabel" name="label_15">
<property name="font">
<font>
@@ -568,7 +477,7 @@ If multiple, input as comma separated.</string>
</property>
</widget>
</item>
- <item row="10" column="1">
+ <item row="8" column="1">
<widget class="QPlainTextEdit" name="uiSummary">
<property name="font">
<font>
diff --git a/lemi2seed/ui_files/stationwidget.ui b/lemi2seed/ui_files/stationwidget.ui
index fc7f75ae4250b8dcb1a5bf72ba8d026f2afacd45..1d4a1beb27d9ca3f51cf5f446c6cb62d44b4ba8b 100644
--- a/lemi2seed/ui_files/stationwidget.ui
+++ b/lemi2seed/ui_files/stationwidget.ui
@@ -109,36 +109,71 @@ Per SEED format requirement, this is a 5-character long string (a-z;A-Z;0-9).</s
</property>
<property name="dateTime">
<datetime>
- <hour>13</hour>
+ <hour>17</hour>
<minute>0</minute>
<second>0</second>
- <year>2021</year>
- <month>1</month>
- <day>6</day>
+ <year>1999</year>
+ <month>12</month>
+ <day>31</day>
</datetime>
</property>
<property name="date">
<date>
- <year>2021</year>
- <month>1</month>
- <day>6</day>
+ <year>1999</year>
+ <month>12</month>
+ <day>31</day>
</date>
</property>
+ <property name="time">
+ <time>
+ <hour>17</hour>
+ <minute>0</minute>
+ <second>0</second>
+ </time>
+ </property>
<property name="maximumDateTime">
<datetime>
- <hour>19</hour>
+ <hour>11</hour>
<minute>59</minute>
<second>59</second>
- <year>7999</year>
+ <year>2999</year>
<month>12</month>
- <day>6</day>
+ <day>31</day>
</datetime>
</property>
+ <property name="maximumDate">
+ <date>
+ <year>2999</year>
+ <month>12</month>
+ <day>31</day>
+ </date>
+ </property>
+ <property name="minimumDate">
+ <date>
+ <year>1999</year>
+ <month>12</month>
+ <day>31</day>
+ </date>
+ </property>
+ <property name="maximumTime">
+ <time>
+ <hour>11</hour>
+ <minute>59</minute>
+ <second>59</second>
+ </time>
+ </property>
+ <property name="minimumTime">
+ <time>
+ <hour>17</hour>
+ <minute>0</minute>
+ <second>0</second>
+ </time>
+ </property>
<property name="currentSection">
<enum>QDateTimeEdit::YearSection</enum>
</property>
<property name="displayFormat">
- <string>yyyy-MM-dd HH-mm-ss</string>
+ <string>yyyy-MM-dd HH:mm:ss</string>
</property>
<property name="calendarPopup">
<bool>true</bool>
@@ -180,26 +215,40 @@ Per SEED format requirement, this is a 5-character long string (a-z;A-Z;0-9).</s
</property>
<property name="dateTime">
<datetime>
- <hour>13</hour>
- <minute>0</minute>
- <second>0</second>
- <year>2021</year>
- <month>1</month>
- <day>7</day>
+ <hour>16</hour>
+ <minute>59</minute>
+ <second>59</second>
+ <year>2999</year>
+ <month>12</month>
+ <day>31</day>
</datetime>
</property>
<property name="date">
<date>
- <year>2021</year>
- <month>1</month>
- <day>7</day>
+ <year>2999</year>
+ <month>12</month>
+ <day>31</day>
</date>
</property>
+ <property name="time">
+ <time>
+ <hour>16</hour>
+ <minute>59</minute>
+ <second>59</second>
+ </time>
+ </property>
+ <property name="maximumTime">
+ <time>
+ <hour>16</hour>
+ <minute>59</minute>
+ <second>59</second>
+ </time>
+ </property>
<property name="currentSection">
<enum>QDateTimeEdit::YearSection</enum>
</property>
<property name="displayFormat">
- <string>yyyy-MM-dd HH-mm-ss</string>
+ <string>yyyy-MM-dd HH:mm:ss</string>
</property>
<property name="calendarPopup">
<bool>true</bool>
@@ -210,56 +259,6 @@ Per SEED format requirement, this is a 5-character long string (a-z;A-Z;0-9).</s
</widget>
</item>
<item row="3" column="0">
- <widget class="QLabel" name="label_5">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Preferred">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="toolTip">
- <string>Are the access to the data at the station level open, partially open or closed?</string>
- </property>
- <property name="text">
- <string>Restricted status</string>
- </property>
- </widget>
- </item>
- <item row="3" column="1">
- <widget class="QComboBox" name="uiRestrictedStatus">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="font">
- <font>
- <weight>50</weight>
- <bold>false</bold>
- </font>
- </property>
- <property name="focusPolicy">
- <enum>Qt::StrongFocus</enum>
- </property>
- <item>
- <property name="text">
- <string>open</string>
- </property>
- </item>
- <item>
- <property name="text">
- <string>partial</string>
- </property>
- </item>
- <item>
- <property name="text">
- <string>closed</string>
- </property>
- </item>
- </widget>
- </item>
- <item row="4" column="0">
<widget class="QLabel" name="label_8">
<property name="toolTip">
<string>Closest geographic name to the station.
@@ -271,7 +270,7 @@ Ex: Whitehorse, YK.</string>
</property>
</widget>
</item>
- <item row="4" column="1">
+ <item row="3" column="1">
<widget class="QLineEdit" name="uiGeoName">
<property name="font">
<font>
@@ -281,7 +280,7 @@ Ex: Whitehorse, YK.</string>
</property>
</widget>
</item>
- <item row="5" column="0">
+ <item row="4" column="0">
<widget class="QLabel" name="label_16">
<property name="toolTip">
<string>Latitude of station location in decimal degrees.</string>
@@ -291,7 +290,7 @@ Ex: Whitehorse, YK.</string>
</property>
</widget>
</item>
- <item row="5" column="1">
+ <item row="4" column="1">
<widget class="QLineEdit" name="uiLat">
<property name="font">
<font>
@@ -301,7 +300,7 @@ Ex: Whitehorse, YK.</string>
</property>
</widget>
</item>
- <item row="6" column="0">
+ <item row="5" column="0">
<widget class="QLabel" name="label_17">
<property name="toolTip">
<string>Longitude of station location in decimal degrees.</string>
@@ -311,7 +310,7 @@ Ex: Whitehorse, YK.</string>
</property>
</widget>
</item>
- <item row="6" column="1">
+ <item row="5" column="1">
<widget class="QLineEdit" name="uiLon">
<property name="font">
<font>
@@ -321,7 +320,7 @@ Ex: Whitehorse, YK.</string>
</property>
</widget>
</item>
- <item row="7" column="0">
+ <item row="6" column="0">
<widget class="QLabel" name="label_18">
<property name="toolTip">
<string>Elevation of station location in meters.</string>
@@ -331,7 +330,7 @@ Ex: Whitehorse, YK.</string>
</property>
</widget>
</item>
- <item row="7" column="1">
+ <item row="6" column="1">
<widget class="QLineEdit" name="uiElev">
<property name="font">
<font>
@@ -341,7 +340,7 @@ Ex: Whitehorse, YK.</string>
</property>
</widget>
</item>
- <item row="8" column="0">
+ <item row="7" column="0">
<widget class="QLabel" name="label_19">
<property name="toolTip">
<string>Declination angle relative to geographic north.
@@ -353,7 +352,7 @@ In decimal degrees.</string>
</property>
</widget>
</item>
- <item row="8" column="1">
+ <item row="7" column="1">
<widget class="QLineEdit" name="uiDeclinationVal">
<property name="font">
<font>
@@ -363,7 +362,7 @@ In decimal degrees.</string>
</property>
</widget>
</item>
- <item row="9" column="0">
+ <item row="8" column="0">
<widget class="QLabel" name="label_20">
<property name="toolTip">
<string>Name of the geomagnetic reference model.</string>
@@ -373,7 +372,7 @@ In decimal degrees.</string>
</property>
</widget>
</item>
- <item row="9" column="1">
+ <item row="8" column="1">
<widget class="QComboBox" name="uiDeclinationModel">
<property name="sizePolicy">
<sizepolicy hsizetype="Expanding" vsizetype="Fixed">
@@ -425,7 +424,7 @@ In decimal degrees.</string>
</item>
</widget>
</item>
- <item row="10" column="0">
+ <item row="9" column="0">
<widget class="QLabel" name="label_21">
<property name="toolTip">
<string>Reference frame for station layout.
@@ -437,7 +436,7 @@ Both assume a right-handed coordinate system with North=0, E=90 and vertical pos
</property>
</widget>
</item>
- <item row="10" column="1">
+ <item row="9" column="1">
<widget class="QComboBox" name="uiOrientationReferenceFrame">
<property name="sizePolicy">
<sizepolicy hsizetype="Expanding" vsizetype="Fixed">
@@ -466,7 +465,7 @@ Both assume a right-handed coordinate system with North=0, E=90 and vertical pos
</item>
</widget>
</item>
- <item row="11" column="0">
+ <item row="10" column="0">
<widget class="QLabel" name="label_22">
<property name="toolTip">
<string>Method for orienting station channels.</string>
@@ -476,7 +475,7 @@ Both assume a right-handed coordinate system with North=0, E=90 and vertical pos
</property>
</widget>
</item>
- <item row="11" column="1">
+ <item row="10" column="1">
<widget class="QComboBox" name="uiOrientationMethod">
<property name="sizePolicy">
<sizepolicy hsizetype="Expanding" vsizetype="Fixed">
@@ -520,7 +519,7 @@ Both assume a right-handed coordinate system with North=0, E=90 and vertical pos
</item>
</widget>
</item>
- <item row="12" column="0">
+ <item row="11" column="0">
<widget class="QLabel" name="label_4">
<property name="sizePolicy">
<sizepolicy hsizetype="Preferred" vsizetype="Preferred">
@@ -545,7 +544,7 @@ Both assume a right-handed coordinate system with North=0, E=90 and vertical pos
</property>
</widget>
</item>
- <item row="12" column="1">
+ <item row="11" column="1">
<widget class="QPlainTextEdit" name="uiComments">
<property name="sizePolicy">
<sizepolicy hsizetype="Expanding" vsizetype="Expanding">
@@ -615,32 +614,6 @@ Both assume a right-handed coordinate system with North=0, E=90 and vertical pos
</widget>
</item>
<item row="1" column="0">
- <widget class="QLabel" name="label_13">
- <property name="font">
- <font>
- <weight>50</weight>
- <bold>false</bold>
- </font>
- </property>
- <property name="toolTip">
- <string>Email of the person submitting the data to the archive.</string>
- </property>
- <property name="text">
- <string>Submitter - Email</string>
- </property>
- </widget>
- </item>
- <item row="1" column="1">
- <widget class="QLineEdit" name="uiSubmitterEmail">
- <property name="font">
- <font>
- <weight>50</weight>
- <bold>false</bold>
- </font>
- </property>
- </widget>
- </item>
- <item row="2" column="0">
<widget class="QLabel" name="label_14">
<property name="font">
<font>
@@ -656,7 +629,7 @@ Both assume a right-handed coordinate system with North=0, E=90 and vertical pos
</property>
</widget>
</item>
- <item row="2" column="1">
+ <item row="1" column="1">
<widget class="QLineEdit" name="uiSubmitterOrganization">
<property name="font">
<font>
diff --git a/setup.py b/setup.py
index bab8320bd5c61db377b71fc49632424d81240727..9d33164fb59ea6db67f35ff89dced2681ef174fb 100644
--- a/setup.py
+++ b/setup.py
@@ -52,6 +52,6 @@ setup(
name='lemi2seed',
packages=find_packages(include=['lemi2seed']),
url='https://git.passcal.nmt.edu/software_public/mt/lemi2seed',
- version='2022.319',
+ version='2023.1.3.1',
zip_safe=False,
)
diff --git a/tests/test_data/METADATA/LEMI_Install_Sheet.xlsx b/tests/test_data/METADATA/LEMI_Install_Sheet.xlsx
index 36b7792a40696fc45beaa11c7c6dfaef597d5925..9f8a57ff8fc57beebc5a840a980a0f497f1e5c3f 100644
Binary files a/tests/test_data/METADATA/LEMI_Install_Sheet.xlsx and b/tests/test_data/METADATA/LEMI_Install_Sheet.xlsx differ
diff --git a/tests/test_data/METADATA/gui_metadata_not_populated.pkl b/tests/test_data/METADATA/gui_metadata_not_populated.pkl
index e6a7f8dbfcde02a46758bbc906ee099b756bf4b3..2ca79bc00cc11c3d00a664b352bf11e2e28b0f97 100644
Binary files a/tests/test_data/METADATA/gui_metadata_not_populated.pkl and b/tests/test_data/METADATA/gui_metadata_not_populated.pkl differ
diff --git a/tests/test_data/METADATA/gui_metadata_populated.pkl b/tests/test_data/METADATA/gui_metadata_populated.pkl
index 19a3fbf69f55b432a525d6d22db7f1159e731798..5656ca7504f27f654b7bd0a75ac1ecf1ba26b3c8 100644
Binary files a/tests/test_data/METADATA/gui_metadata_populated.pkl and b/tests/test_data/METADATA/gui_metadata_populated.pkl differ
diff --git a/tests/test_data/METADATA/metadata_fields.pkl b/tests/test_data/METADATA/metadata_fields.pkl
index 53bfb233cfd4b63fc9071f754b0aa48148545974..bac33a8640224dd089a173dd215d98a3107f32e8 100644
Binary files a/tests/test_data/METADATA/metadata_fields.pkl and b/tests/test_data/METADATA/metadata_fields.pkl differ
diff --git a/tests/test_data/METADATA/metadata_fields_reformatted.pkl b/tests/test_data/METADATA/metadata_fields_reformatted.pkl
index 9e4d38933281204ec66ce3b6451280d66ed13825..ce9312bcd6cce54754e8d5521c729c40bd613b9b 100644
Binary files a/tests/test_data/METADATA/metadata_fields_reformatted.pkl and b/tests/test_data/METADATA/metadata_fields_reformatted.pkl differ
diff --git a/tests/test_data/STATIONXML/network.pkl b/tests/test_data/STATIONXML/network.pkl
index 10c3921db9b93a38c2eb14232e882f436d10baa1..7d8a0d13b98fe90e0c52ebcc4ca400751d4056aa 100644
Binary files a/tests/test_data/STATIONXML/network.pkl and b/tests/test_data/STATIONXML/network.pkl differ
diff --git a/tests/test_data/STATIONXML/station.pkl b/tests/test_data/STATIONXML/station.pkl
index c4126cce9e4df1b47f1d6e5b6a1036a2dfb59a55..134a2b8b715cd5ae7222bb85e861c712b4452c9c 100644
Binary files a/tests/test_data/STATIONXML/station.pkl and b/tests/test_data/STATIONXML/station.pkl differ
diff --git a/tests/test_data/STATIONXML/updated_electric_channel.pkl b/tests/test_data/STATIONXML/updated_electric_channel.pkl
index 6fb8190bf1ce5ed71638cf24de19a07bf40d1902..01b7ebca8497fc36085bc662878aa2a262f29cb2 100644
Binary files a/tests/test_data/STATIONXML/updated_electric_channel.pkl and b/tests/test_data/STATIONXML/updated_electric_channel.pkl differ
diff --git a/tests/test_lemi2seed.py b/tests/test_lemi2seed.py
index 1ba447e4feeb4f861458ccb89f2602790bb4d129..5fb2ef306108a73a409ebba2a8b1e56103deeb1f 100644
--- a/tests/test_lemi2seed.py
+++ b/tests/test_lemi2seed.py
@@ -27,6 +27,7 @@ class TestArgsFunctions(unittest.TestCase):
"""Set up test fixtures."""
self.path2data = TEST_DIR.joinpath("EM", "TEST1")
self.path2metadata = TEST_DIR.joinpath("METADATA")
+ self.path2savedmd = TEST_DIR.joinpath("METADATA", "gui_metadata_populated.pkl")
self.output_mseed = Path(__file__).resolve().parent.joinpath('MSEED')
def test_check_output_dir_creation(self):
@@ -64,7 +65,7 @@ class TestArgsFunctions(unittest.TestCase):
with self.assertRaises(SystemExit) as cmd2:
get_args()
msg = ("lemi2seed cannot run under both the 'quality control' and "
- "'gui only' mode at the same time. Try --help option or choose "
+ "'gui only' mode at the same time! Try --help option or choose "
"one or the other mode.")
self.assertEqual(cmd1.output, [":".join(['ERROR', SCR_DIR, msg])])
self.assertEqual(cmd2.exception.code, 1)
@@ -87,8 +88,8 @@ class TestArgsFunctions(unittest.TestCase):
with self.assertLogs(logger, level='INFO') as cmd:
with patch("lemi2seed.lemi2seed.Path.mkdir"):
_, path2metadata, *other = get_args()
- msg = ("Running lemi2seed in 'quality control' mode. Handling of "
- "metadata will be bypassed.")
+ msg = ("Handling of the field sheets is bypassed when running in "
+ "'quality control' mode.")
self.assertEqual(cmd.output, [":".join(['INFO', SCR_DIR, msg])])
self.assertIsNone(path2metadata)
@@ -99,8 +100,8 @@ class TestArgsFunctions(unittest.TestCase):
with self.assertLogs(logger, level='INFO') as cmd:
with patch("lemi2seed.lemi2seed.Path.mkdir"):
_, path2metadata, *other = get_args()
- msg = ("Running lemi2seed in 'gui only' mode. All metadata should be "
- "entered using the GUI. Bypassing the use of field sheets.")
+ msg = ("All metadata should be entered using the GUI in 'gui only' "
+ "mode. Bypassing the use of field sheets.")
self.assertEqual(cmd.output, [":".join(['INFO', SCR_DIR, msg])])
self.assertIsNone(path2metadata)
@@ -124,7 +125,7 @@ class TestArgsFunctions(unittest.TestCase):
_, path2metadata, *other = get_args()
msg1 = "The path to the LEMI field spreadsheets does not exist!"
msg2 = ("In 'quality control' or 'gui only' mode, field sheets are not "
- "parsed!")
+ "parsed.")
self.assertEqual(cmd.output[0], ":".join(['ERROR', SCR_DIR, msg1]))
self.assertEqual(cmd.output[1], ":".join(['INFO', SCR_DIR, msg2]))
self.assertIsNone(path2metadata)
@@ -138,7 +139,7 @@ class TestArgsFunctions(unittest.TestCase):
_, path2metadata, *other = get_args()
msg1 = "The path to the LEMI field spreadsheets does not exist!"
msg2 = ("In 'quality control' or 'gui only' mode, field sheets are not "
- "parsed!")
+ "parsed.")
self.assertEqual(cmd.output[0], ":".join(['ERROR', SCR_DIR, msg1]))
self.assertEqual(cmd.output[1], ":".join(['INFO', SCR_DIR, msg2]))
self.assertIsNone(path2metadata)
@@ -157,6 +158,49 @@ class TestArgsFunctions(unittest.TestCase):
self.assertEqual(cmd1.output[1], ":".join(['ERROR', SCR_DIR, msg2]))
self.assertEqual(cmd2.exception.code, 1)
+ def test_get_args_path2savedmd_qc_only(self):
+ """Test basic functionality of get_args."""
+ with patch("sys.argv", ["lemi2seed", "-d" + str(self.path2data),
+ "-s" + str(self.path2savedmd), "-qc"]):
+ with self.assertLogs(logger, level='INFO') as cmd:
+ _, _, path2savedmd, *other = get_args()
+ msg = ("Handling of previously saved metadata is bypassed when running "
+ "in 'quality control' mode.")
+ self.assertEqual(cmd.output[0], ":".join(['INFO', SCR_DIR, msg]))
+ self.assertIsNone(path2savedmd)
+
+ def test_get_args_path2savedmd_do_not_exist(self):
+ """Test basic functionality of get_args."""
+ with patch("sys.argv", ["lemi2seed", "-d" + str(self.path2data),
+ "-s" + str(self.path2savedmd) + "_", "-g"]):
+ with self.assertLogs(logger, level='ERROR') as cmd:
+ _, _, path2savedmd, *other = get_args()
+ msg = ("The provided path to a previously saved metadata file (*.pkl) "
+ "does not exist! Bypassing loading of metadata fields "
+ "before launching the GUI.")
+ self.assertEqual(cmd.output[0], ":".join(['ERROR', SCR_DIR, msg]))
+ self.assertIsNone(path2savedmd)
+
+ def test_get_args_path2savedmd_gui_only(self):
+ """Test basic functionality of get_args."""
+ with patch("sys.argv", ["lemi2seed", "-d" + str(self.path2data),
+ "-s" + str(self.path2savedmd), "-g"]):
+ _, _, path2savedmd, *other = get_args()
+ self.assertEqual(path2savedmd, self.path2savedmd)
+
+ def test_get_args_path2savedmd_field_sheet_and_gui(self):
+ """Test basic functionality of get_args."""
+ with patch("sys.argv", ["lemi2seed", "-d" + str(self.path2data),
+ "-m" + str(self.path2metadata),
+ "-s" + str(self.path2savedmd)]):
+ with self.assertLogs(logger, level='INFO') as cmd:
+ _, _, path2savedmd, *other = get_args()
+ msg = ("The loading of a previously saved metadata file (*.pkl) is "
+ "bypassed when running in 'field sheet and gui' mode. Try "
+ "--help option for more information.")
+ self.assertEqual(cmd.output[0], ":".join(['INFO', SCR_DIR, msg]))
+ self.assertIsNone(path2savedmd)
+
def test_get_args_output_xml_none(self):
"""Test basic functionality of get_args."""
with patch("sys.argv", ["lemi2seed", "-d" + str(self.path2data), "-qc"]):
@@ -298,6 +342,8 @@ class TestMain(unittest.TestCase):
main()
expected_msg = ["INFO:lemi2seed.lemi2seed:Running lemi2seed in "
"'field sheet and gui' mode.", "INFO:lemi2seed."
- "lemi2seed:Launching the GUI."]
+ "lemi2seed:Pre-populating the GUI metadata fields "
+ "using the information provided in the field sheet(s).",
+ "INFO:lemi2seed.lemi2seed:Launching the GUI."]
self.assertEqual(cmd.output, expected_msg)
self.assertEqual(mock_gui.call_count, 1)
diff --git a/tests/test_lemi_metadata.py b/tests/test_lemi_metadata.py
index 6995212124da364359c7fc93efc43a88b1f550b6..84403520ff398deb8bff61207e0cdcb51d29bdaf 100644
--- a/tests/test_lemi_metadata.py
+++ b/tests/test_lemi_metadata.py
@@ -98,7 +98,6 @@ class TestLemiMetadata(unittest.TestCase):
def test_reformat_run(self):
"""Test basic functionality of reformat_run."""
run_fields = self.md_fields_no_reformat['Run']
-
file_ = self.path2md.joinpath('run_fields_reformatted.pkl')
with open(file_, 'rb') as fin:
reformatted = pickle.load(fin)
@@ -141,7 +140,7 @@ class TestLemiMetadata(unittest.TestCase):
self.md.from_field_sheets
msg = ("Already parsed the install sheet - You may have more than one "
"install sheet - Skipping {}!".format(self.file))
- self.assertEqual(cmd.output, [":".join(['WARNING', SCR_DIR, msg])])
+ self.assertEqual(cmd.output[0], ":".join(['WARNING', SCR_DIR, msg]))
def test_from_field_sheets_expected_workflow(self):
"""Test basic functionality of from_field_sheets"""
@@ -162,14 +161,14 @@ class TestLemiMetadata(unittest.TestCase):
"""Test basic functionality of populate_sta_props."""
self.md.populate_sta_props(self.md_fields['Sta'])
self.assertSetEqual(self.md.sta.md_missing,
- {'end', 'elev', 'lon', 'start', 'geo_name'})
- self.assertSetEqual(self.md.sta.md_invalid, {'elev', 'lon', 'start'})
+ {'end', 'start', 'geo_name'})
+ self.assertSetEqual(self.md.sta.md_invalid, {'end', 'start'})
for key, val in self.md_fields['Sta'].items():
if key not in self.md.sta.md_invalid:
self.assertEqual(getattr(self.md.sta, key), val)
self.assertEqual(self.md.sta.run_list, 'a, b, c, d')
- self.assertIsNone(self.md.sta.elev)
self.assertIsNone(self.md.sta.start)
+ self.assertIsNone(self.md.sta.end)
def test_init_run_props(self):
"""Test basic functionality of init_run_props."""
@@ -311,13 +310,8 @@ class TestLemiMetadata(unittest.TestCase):
type_ = 'E'
run_id = 'b'
self.md.populate_run_props(self.md_fields['Run'])
- with self.assertLogs(logger, level='WARNING') as cmd:
- self.md.get_comps_rec(type_, run_id)
- msg = (f"No set of recorded components found for run '{run_id}'. "
- "If you did record electric field data for that run, please "
- "update the 'components recorded' metadata field at the "
- "Station/Runs level!")
- self.assertEqual(cmd.output, [":".join(['WARNING', SCR_DIR, msg])])
+ comps_rec = self.md.get_comps_rec(type_, run_id)
+ self.assertListEqual(comps_rec, [])
def test_get_comps_rec_no_elec_but_mag(self):
"""Test basic functionality of get_comps_rec."""
diff --git a/tests/test_metadata_category.py b/tests/test_metadata_category.py
index 27306d517f77dc7e77310aff40a25e5841fb9440..c93df95b96fc2a15819e2ddb0bf1eb24c9a8bf86 100644
--- a/tests/test_metadata_category.py
+++ b/tests/test_metadata_category.py
@@ -104,76 +104,6 @@ class TestNet(unittest.TestCase):
"""Test basic functionality of validate_archive_net."""
self.assertTrue(Net.validate_archive_net('EM'))
- def test_validate_citation_dataset_doi_undefined(self):
- """Test basic functionality of validate_citation_dataset_doi."""
- doi = None
- self.assertTrue(Net.validate_citation_dataset_doi(doi))
-
- def test_validate_citation_dataset_doi_erroneous_type(self):
- """Test basic functionality of validate_citation_dataset_doi."""
- with self.assertLogs(logger, level='ERROR') as cmd:
- Net.validate_citation_dataset_doi(10.7914)
- msg = "The DOI number(s) should be a string."
- self.assertEqual(cmd.output, [":".join(['ERROR', SCR_DIR, msg])])
-
- def test_validate_citation_dataset_doi_invalid_doi(self):
- """Test basic functionality of validate_citation_dataset_doi."""
- with self.assertLogs(logger, level='ERROR') as cmd:
- Net.validate_citation_dataset_doi('10.7914/SN/EM')
- msg = ("Invalid DOI(s). The DOI number(s) provided by the archive "
- "should be strings formatted as follows: 'scheme: path'.")
- self.assertEqual(cmd.output, [":".join(['ERROR', SCR_DIR, msg])])
-
- def test_validate_citation_dataset_doi_invalid_dois(self):
- """Test basic functionality of validate_citation_dataset_doi."""
- dois = '10.7914/SN/EM, DOI:10.3421/SN/EG'
- with self.assertLogs(logger, level='ERROR') as cmd:
- Net.validate_citation_dataset_doi(dois)
- msg = ("Invalid DOI(s). The DOI number(s) provided by the archive "
- "should be strings formatted as follows: 'scheme: path'.")
- self.assertEqual(cmd.output, [":".join(['ERROR', SCR_DIR, msg])])
-
- def test_validate_citation_dataset_doi_valid_doi(self):
- """Test basic functionality of validate_citation_dataset_doi."""
- doi = 'DOI:10.7914/SN/EM'
- self.assertTrue(Net.validate_citation_dataset_doi(doi))
-
- def test_validate_citation_dataset_doi_valid_dois(self):
- """Test basic functionality of validate_citation_dataset_doi."""
- dois = 'DOI:10.7914/SN/EM, DOI:10.3421/SN/EG'
- self.assertTrue(Net.validate_citation_dataset_doi(dois))
-
- def test_validate_project_lead_email_undefined(self):
- """Test basic functionality of validate_project_lead_email."""
- self.assertTrue(Net.validate_project_lead_email(None))
-
- def test_validate_project_lead_email_erroneous_type(self):
- """Test basic functionality of validate_project_lead_email."""
- with self.assertLogs(logger, level='ERROR') as cmd:
- Net.validate_project_lead_email(12)
- msg = "The project lead email(s) should be a string."
- self.assertEqual(cmd.output, [":".join(['ERROR', SCR_DIR, msg])])
-
- def test_validate_project_lead_email_invalid_email(self):
- """Test basic functionality of validate_project_lead_email."""
- email = 'mpasscal.edu'
- self.assertFalse(Net.validate_project_lead_email(email))
-
- def test_validate_project_lead_email_invalid_emails(self):
- """Test basic functionality of validate_project_lead_email."""
- emails = 'mpasscal.edu, d@passcal.edu'
- self.assertFalse(Net.validate_project_lead_email(emails))
-
- def test_validate_project_lead_email_valid_email(self):
- """Test basic functionality of validate_citation_dataset_doi."""
- email = 'm@passcal.edu'
- self.assertTrue(Net.validate_project_lead_email(email))
-
- def test_validate_project_lead_email_valid_emails(self):
- """Test basic functionality of validate_citation_dataset_doi."""
- emails = 'm@passcal.edu, d@passcal.edu'
- self.assertTrue(Net.validate_project_lead_email(emails))
-
class TestBaseSta(unittest.TestCase):
"""Test suite for BaseSta data class."""
@@ -181,7 +111,7 @@ class TestBaseSta(unittest.TestCase):
def setUp(self):
"""Set up test fixtures"""
data_input = 2201.77
- min_elev, max_elev = [abs(data_input) * x for x in [0.99, 1.01]]
+ min_elev, max_elev = [data_input + x for x in [-100, 100]]
param = ("station elevation", -500, 8500, min_elev, max_elev, data_input, 'm')
self.param = param
@@ -210,12 +140,14 @@ class TestBaseSta(unittest.TestCase):
def test_validate_geos_do_not_match_logger_recorded_metadata(self):
"""Test basic functionality of validate_geos."""
- geo, _, _, _, _, val, units = self.param
- with self.assertLogs(logger, level='ERROR') as cmd:
- BaseSta.validate_geos(self.param, 2250)
+ geo, _, _, _, max_val, val, units = self.param
+ with self.assertLogs(logger, level='WARNING') as cmd:
+ BaseSta.validate_geos(self.param, 2350)
+ tolerance = max_val - val
msg = ("Unexpected {0}! Provided {0} should roughly match the {0} "
- "recorded by the on-site GPS ({1:.3f}{2}).".format(geo, val, units))
- self.assertEqual(cmd.output, [":".join(['ERROR', SCR_DIR, msg])])
+ "recorded by the on-site GPS ({1:.3f} ± {2:.3f}{3})."
+ .format(geo, val, tolerance, units))
+ self.assertEqual(cmd.output, [":".join(['WARNING', SCR_DIR, msg])])
class TestSta(unittest.TestCase):
@@ -247,10 +179,6 @@ class TestSta(unittest.TestCase):
"""Test basic functionality of validate_archive_id."""
self.assertTrue(Sta.validate_archive_id('KELLY'))
- def test_validate_submitter_email_undefined(self):
- """Test basic functionality of validate_submitter_email."""
- self.assertTrue(Sta.validate_submitter_email(None))
-
class TestRun(unittest.TestCase):
"""Test suite for Run data class."""
@@ -266,16 +194,16 @@ class TestRun(unittest.TestCase):
"""Test basic functionality of validate_comps_rec."""
with self.assertLogs(logger, level='ERROR') as cmd:
self.run.validate_comps_rec(None)
- msg = ("The list of components recorded for run '{}' should be a "
- "string. Example: {}".format(self.run.run_id, VALID_COMPS[0]))
+ msg = ("The 'components recorded' metadata field is empty for run '{}'. "
+ "Example of valid field: {}".format(self.run.run_id, VALID_COMPS[0]))
self.assertEqual(cmd.output, [":".join(['ERROR', SCR_DIR, msg])])
def test_validate_comps_rec_erroneous_type(self):
"""Test basic functionality of validate_comps_rec."""
with self.assertLogs(logger, level='ERROR') as cmd:
self.run.validate_comps_rec(12)
- msg = ("The list of components recorded for run '{}' should be a "
- "string. Example: {}".format(self.run.run_id, VALID_COMPS[0]))
+ msg = ("The 'components recorded' metadata field is empty for run '{}'. "
+ "Example of valid field: {}".format(self.run.run_id, VALID_COMPS[0]))
self.assertEqual(cmd.output, [":".join(['ERROR', SCR_DIR, msg])])
def test_validate_comps_rec_invalid_magnetic_channel(self):
diff --git a/tests/test_metadata_conversion.py b/tests/test_metadata_conversion.py
index 0ee9b81843936d9795739ca9747ac459965c97f5..fb79efc2bd5b0b02b0b5e1f79476fcea594d72d5 100644
--- a/tests/test_metadata_conversion.py
+++ b/tests/test_metadata_conversion.py
@@ -50,16 +50,16 @@ class TestGetXmlFieldGetComment(unittest.TestCase):
def test_get_xml_field(self):
"""Test basic functionality of get_xml_field."""
- field_info, field_value = get_xml_field(self.md.net, self.net_fields[1])
+ field_info, field_value = get_xml_field(self.md.net, self.net_fields[0])
self.assertListEqual(field_info, ['end_date'])
self.assertEqual(field_value, UTCDateTime('2021-03-02T00:00:00.000000Z'))
- field_info, field_value = get_xml_field(self.md.net, self.net_fields[6])
+ field_info, field_value = get_xml_field(self.md.net, self.net_fields[4])
self.assertListEqual(field_info, ['comments', 'mt.network.comments'])
self.assertEqual(field_value, 'Network Test')
def test_get_comment_no_run_id_considered(self):
"""Test basic functionality of get_comment."""
- field_info, field_value = get_xml_field(self.md.net, self.net_fields[6])
+ field_info, field_value = get_xml_field(self.md.net, self.net_fields[4])
comment = get_comment(field_info, field_value)
self.assertEqual(comment.value, 'Network Test')
self.assertEqual(comment.subject, 'mt.network.comments')
@@ -103,13 +103,10 @@ class TestCreateInventoryObjects(unittest.TestCase):
"""Test basic functionality of create_net."""
net = self.md.net
net.start = UTCDateTime(2020, 10, 1, 0, 0)
- net.restricted_status = 'open'
net.project = 'PIS_MT'
net.project_lead_author = 'Maeva Pourpoint'
- net.project_lead_email = 'm@passcal.edu'
net.project_lead_organization = 'PASSCAL'
net.acquired_by_author = 'Maeva Pourpoint'
- net.citation_dataset_doi = 'DOI:10.7914/SN/EM, DOI:10.3421/SN/EG'
net.country = 'USA'
net.geo_name = 'Southwest'
net.name = 'MT experiment in Kelly ranch'
@@ -123,12 +120,10 @@ class TestCreateInventoryObjects(unittest.TestCase):
sta = self.md.sta
sta.start = UTCDateTime(2020, 9, 30, 0, 0)
sta.end = UTCDateTime(2020, 10, 2, 0, 0)
- sta.restricted_status = 'open'
sta.lon = -107.13
sta.elev = 2201
- sta.software_version = '2021.320'
+ sta.software_version = '2022.332'
sta.submitter_author = 'David Goldak'
- sta.submitter_email = 'dgoldak@passcal.nmt.edu'
sta.submitter_organization = 'PASSCAL'
runs = self.md.run
runs[0].md_by_author = 'Tom'